WO2022058700A1 - Treatment of idiopathic pulmonary fibrosis - Google Patents
Treatment of idiopathic pulmonary fibrosis Download PDFInfo
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- WO2022058700A1 WO2022058700A1 PCT/GB2020/052218 GB2020052218W WO2022058700A1 WO 2022058700 A1 WO2022058700 A1 WO 2022058700A1 GB 2020052218 W GB2020052218 W GB 2020052218W WO 2022058700 A1 WO2022058700 A1 WO 2022058700A1
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Definitions
- the invention generally relates to products for use in the treatment and/or prevention of tissue fibrosis, and to methods of identifying agents which inhibit tissue fibrosis. More specifically, the invention relates to agents that inhibit succinate dehydrogenase, and monocyte-recruited macrophage populations, for use in the treatment and/or prevention of tissue fibrosis.
- Idiopathic pulmonary fibrosis is a chronic debilitating lung disease, characterized by the deposition of excessive extracellular matrix in the lung parenchyma.
- Existing pharmacological options are limited and with an increasing worldwide incidence and a median survival of 3 years from diagnosis, there is an urgent requirement to understand pathological mechanisms involved and to provide effective treatments.
- AMs airway macrophages
- IPF airway macrophages
- AMs are crucial in contributing to pulmonary defence, repair, surfactant processing and inflammatory responses.
- AMs are strategically positioned at the interface between the airways and the environment and are found in the alveoli and airways, secreting numerous pro-fibrotic soluble mediators, chemokines, and matrix metalloproteases.
- Macrophages demonstrate remarkable plasticity and are capable of acquiring phenotypes which can both drive or resolve fibro-proliferative responses to injury.
- AMs have been shown to be involved in the regulation of the extracellular matrix via secretion of matrix metalloproteases (MMPs) or by direct uptake of collagen.
- MMPs matrix metalloproteases
- Macrophage activation is tightly linked to cellular metabolism. Inflammatory activation of macrophages results in impaired mitochondrial respiration and tricarboxylic acid (TCA) cycle disruption, resulting in the accumulation of endogenous metabolites capable of adopting immunomodulatory roles.
- TCA tricarboxylic acid
- One such bioactive metabolite is itaconate.
- CAD cis-aconitate decarboxylase
- ACOD1 aconitate decarboxylase 1
- Itaconate is one of the most highly induced metabolites in activated bone marrow-derived macrophages and can suppress the expression of pro-inflammatory cytokines. Furthermore, itaconate has been shown to control macrophage effector functions via competitive inhibition of succinate dehydrogenase (SDH) mediated oxidation of succinate and furthermore, drives an anti-inflammatory program via the KEAP-1-NRF2 axis. Therefore, itaconate appears to be a crucial regulator of macrophage phenotype and function. However, its functional significance in specialized tissue resident macrophages during chronic respiratory disease such as IPF remains unknown.
- SDH succinate dehydrogenase
- the inventors have previously linked AM phenotype to disease outcome in IPF, since increased numbers of AMs lacking the transferrin receptor CD71 are associated with worsened disease.
- the inventors have now demonstrated that the ACODl/itaconate axis is an endogenous pulmonary regulatory pathway, which limits fibrosis. Further, the inventors have sown for the first time that itaconate and cis-aconitate decarboxylase have therapeutic potential as targets in IPF and other diseases where fibrosis plays a role, particularly chronic respiratory diseases with a fibrotic component.
- the present inventors have now demonstrated for the first time that the ACODl/itaconate axis is altered in the human lung during IPF, itaconate is an anti-fibrotic factor in the murine lung and that it impairs human fibroblast activity.
- the inventors have also shown that in patients with IPF, there is decreased expression of ACOD1 in AMs and reduced levels of airway itaconate, compared to healthy controls.
- Acodl deficiency in mice leads to more severe disease pathology, which is further exacerbated by adoptive transfer of Acodl-/-, but not WT monocyte- recruited AMs.
- Addition of exogenous itaconate to cultures of human lung fibroblasts limits proliferation and wound healing and furthermore, inhaled itaconate (particularly oropharyngeal inhalation) ameliorates lung fibrosis in mice.
- the invention provides an agent which inhibits succinate dehydrogenase for use in the treatment or prevention of tissue fibrosis.
- the agent which inhibits succinate dehydrogenase may directly inhibit succinate dehydrogenase, wherein optionally the agent is selected from a small molecule compound, a nucleic acid, an antibody or antigen-binding fragment thereof, or an aptamer.
- the agent which inhibits succinate dehydrogenase may indirectly inhibit succinate dehydrogenase, wherein optionally the agent increases the expression and/or activity of aconitate decarboxylase 1 (ACOD1), wherein optionally the agent is a nucleic acid, a protein, or a small molecule,.
- ACOD1 aconitate decarboxylase 1
- the small molecule compound which directly inhibits succinate dehydrogenase may be itaconate or a derivative or analogue thereof, optionally in the form of a pharmaceutically acceptable salt.
- the agent for use in the treatment or prevention of tissue fibrosis may be administered by: inhalation; intraperitoneal, subcutaneous, and/or intramuscular injection; infusion; and/or orally, preferably wherein the agent is administered by oropharyngeal inhalation and/or nasal inhalation.
- the agent for use in the treatment or prevention of tissue fibrosis may be delivered in a drug delivery system, wherein optionally said drug delivery system: a) specifically targets phagocytes; and/or b) is a liposome-based drug delivery system.
- the itaconate, derivative, analogue or pharmaceutically acceptable salt thereof may be administered at a dose of about O.lmg/kg to about lOmg/kg.
- the itaconate, derivative, analogue or pharmaceutically acceptable salt thereof is administered once per week to about four times per day, preferably about once per day.
- the invention also provides a population of monocyte-recruited macrophages (Mo-Ms) for use in the treatment or prevention of tissue fibrosis.
- Mo-Ms monocyte-recruited macrophages
- the Mo-Ms may express Acodl, and optionally have a quiescent metabolic phenotype.
- the population of Mo-Ms may be administered directly to an individual to be treated.
- the population of Mo-Ms may be recruited following administration of a composition which stimulates targeting of Mo-Ms to a tissue to be treated.
- the Mo-Ms may be autologous Mo-Ms or allogenic Mo-Ms.
- the treatment or prevention may modify the metabolic and/or fibrotic phenotype of tissue-resident macrophages (Tr-Ms), preferably wherein the treatment or prevention increases the metabolic phenotype and/or reduces the fibrotic phenotype of the Tr-M.
- Tr-Ms tissue-resident macrophages
- the treatment or prevention may increase the proportion of CDllb7MHCH + Tr-Ms resident in the tissue.
- the treatment or prevention may modify the metabolic and/or fibrotic phenotype of fibroblasts within the tissue, preferably wherein the treatment or prevention reduces the metabolic and/or fibrotic phenotype of the fibroblasts.
- the treatment or prevention may: reduce the oxygen consumption rate, maximal respiration and/or spare respiratory capacity of fibroblasts; reduce proliferation of fibroblasts; and/or reduce the wound healing capacity of fibroblasts.
- the treatment or prevention may result in: an improvement in the fibrosis of the tissue; a decrease in tissue collagen expression, preferably Col3al, Collal and/or Col4al; a decrease in tissue fibronectin (Fnl) expression; a decrease in IL-lfJ expression in fibroblasts obtained from the tissue; and/or a decrease in hydroxyproline levels.
- tissue collagen expression preferably Col3al, Collal and/or Col4al
- Fnl tissue fibronectin
- IL-lfJ IL-lfJ expression in fibroblasts obtained from the tissue
- hydroxyproline levels hydroxyproline levels
- the fibrosis may be pulmonary fibrosis, liver fibrosis, kidney fibrosis, intestinal fibrosis, cardiac fibrosis, myelofibrosis and/or skin fibrosis.
- the pulmonary fibrosis is any form of chronic fibrosing interstitial lung disease including idiopathic pulmonary fibrosis.
- the treatment or prevention according to the invention may result in: a) an improvement in lung function, preferably an increase in forced vital capacity, an increase in total lung capacity and/or an increase in the transfer capacity of the lung for the uptake of carbon monoxide, as measured by gas transfer (TLco) test; b) a reduction in the decline of forced vital capacity; c) preservation or improvement of exercise capacity; d) a reduction in the progression of fibrosis as quantified by high resolution computed tomography; e) preservation or improvement of quality of life; and/or (f) improved survival.
- the agent or population of Mo-Ms for use according to the invention may be for use in an individual having reduced levels of itaconate in a sample of the tissue to be treated, and wherein the tissue fibrosis is pulmonary fibrosis, the sample is optionally a bronchoalveolar lavage (BAL) sample.
- BAL bronchoalveolar lavage
- the agent or population of Mo-Ms may be for use in an individual having Tr-Ms with reduced ACOD1 expression.
- the agent or population of Mo-Ms may be for use in combination with another therapeutic.
- the invention also provides a method for identifying a compound which inhibits fibrosis progression, comprising the steps of: a) culturing cells in vitro; b) adding a test compound to the cultured cells; and c) determining a change in the metabolic phenotype of the cells in response to the test compound; wherein the change in metabolic phenotype of the cells is a reduction or increase in the metabolic phenotype of the cells; wherein preferably the cells are fibroblasts or Tr-Ms.
- a reduction or increase in the metabolic phenotype of the cells may be: a) a reduction or increase in the oxygen consumption rate of the cells; b) a reduction or increase in the maximal respiration of the cells; and/or c) a reduction or increase in the spare respiratory capacity of the cells.
- the method of the invention may further comprise a step of determining a reduction in the fibrotic phenotype of the cells in response to the test compound.
- FIG. 1 The ACODl/itaconate axis is decreased in IPF and Acodl-/- mice have worsened phenotype upon bleomycin exposure.
- C Schematic of dosing regimen.
- WT or Acodl-/- mice were dosed oropharyngeal with 0.05U bleomycin or PBS control at day 0 and harvested at day 7, day 21 or day 42 post bleomycin.
- Figure 2 Acodl-/- mice have worsened fibrotic phenotype at late time point.
- C-D Ashcroft score (C) and representative images (D) of lung slices of PBS or Bleo dosed mice at day 42 post bleomycin stained with Sirius Red, scored blinded by 3-5 individuals.
- FIG. 3 Itaconate controls tissue resident AM metabolism.
- B Energy map of indicating overall energy state of PBS Tr-AM, Bleo Tr-AM and Bleo Mo-AM; four energy states are shown: quiescent, energetic, aerobic and glycolytic. Same n numbers as in A.
- (C) Gene expression analysis of Acodl in BAL PBS Tr-AM, Bleo Tr-AM and Bleo Mo-AM at day 1, day 7 and day 21 (n 4-7 per group) post bleomycin. Actb was used as housekeeping control. Pooled from three independent experiments.
- E Maximal respiration during mitochondrial stress test (D), defined as the maximal oxygen consumption rate after addition of FCCP.
- FIG. 4 Acodl-deficient tissue resident AMs are more pro-fibrotic post bleomycin.
- C-D Heat map representation of murine fibrosis gene array of FACS sorted Mo-AM (C) and Tr-AM (D) from WT and Acodl-/- mice.
- FIG. 5 Adoptive transfer of WT Mo-AMs improves pulmonary fibrosis and rescues tissue resident AM phenotype in Acodl-/- mice post bleomycin.
- A Schematic of dosing regimen and adoptive transfer. WT or Acodl-/- mice were dosed oropharyngeal with 0.05U bleomycin at day 0, Mo-AMs were FACS sorted at day 7 post bleomycin and transferred into Acodl-/- mice via the oropharyngeal route. Mice were then harvested after further 14 days, at day 21 post initial bleomycin exposure.
- (D) Gene expression analysis of Colal, Col3al, Col4al and Fnl in lung homogenate of Acodl-/- mice adoptively transferred with WT or Acodl-/- Mo-AMs (n 3 - 6 per group); day 21 post bleomycin, Actb was used as housekeeping gene.
- E-H Fraction of CDllb+/MHC 11+ and CDllb-/MHC II- Tr-AM (E-F) and Mo-AM (G-H) in BAL of Acodl-/- mice adoptively transferred with WT or Acodl-/- Mo-AMs; day 21 post bleomycin.
- Figure 6 Exogenous itaconate limits human lung fibroblast wound healing.
- B Energy map of (A) showing four energy states during mitochondrial stress test: quiescent, energetic, aerobic and glycolytic. Same n numbers as in A.
- C Maximal respiration and spare respiratory capacity (SRC) during mitochondrial stress test (A). Maximal respiration defined as the maximal oxygen consumption rate after addition of FCCP; SRC defined as subtraction of basal from maximal OCR.
- Figure 7 Inhaled itaconate is anti-fibrotic.
- A Schematic of dosing regime using 8-10 week old C57BI/6 mice. 0.05U Bleomycin or PBS control and 0.25mg/kg itaconate or PBS control was administered oropharyngeal at indicated time points and mice were harvested at day 21 post bleomycin.
- B - C Ashcroft score and representative images (C) of lung slices stained with Sirius Red, scored blinded by 3-5 individuals.
- D Gene expression analysis of Collal, Col3al, Col4al and Fnl in lung homogenate; Actb was used as housekeeping control. Pooled from two independent experiments.
- Figure 8 MACS sorting of human CD206+ BAL AM.
- A Representative FACS plots showing gating strategy to assess purity of human CD45+, CD206+ BAL AM population before and after magnetic activated cell sorting (MACS).
- Figure 9 Gating strategies of murine flow cytometry.
- A Representative FACS plots showing gating strategy to determine the following immune cell populations in murine BAL and lung: eosinophils, monocytes, airway macrophages (AM), including monocyte-recruited AMs (SigFint), and tissueresident AMs (SigFhigh), , neutrophils, dendritic cells (DCs), T cells, including Thl-T-cells, Th2-T-cells and Th-17-T-cells.
- B Representative FACS plots showing gating strategy to determine expression of mitoSOX dye for superoxide in murine BAL CD45+ population.
- Figure 10 Lung function and immune cell profile after bleomycin treatment in Acodl-/- mice.
- (D) Total BAL cells in PBS and bleomycin dosed WT and Acodl-/- mice at day 21 post bleomycin; (n 5 - 10, two experiments pooled).
- Figure 11 Fibrotic phenotype in Acodl-/- mice at day 7 and day 21 post bleomycin.
- Figure 12 Baseline lung function and immune cell recruitment in WT and Acodl-/- mice.
- a - C Resistance (A), elastance (B) and compliance (C) at baseline measured by FlexiVent in PBS dosed WT and Acodl-/- mice at day 7, day 21 and day 42.
- D - F Total BAL cells (D), numbers of BAL AMs (E) and BAL neutrophils (F) in PBS dosed WT and Acodl-/- mice at day 7, day 21 and day 42.
- Figure 13 Itaconate controls tissue resident AM metabolism.
- A Schematic of dosing regimen using 8-10 week old C57BI/6 mice. 0.05U Bleomycin and 0.05pM PKH26 Celltracker was administered oropharyngeal at indicated time points.
- B Representative FACS plots showing gating strategy to assess PKH-26 Celltracker in Tr-AM and Mo-AM populations (see gating strategy Figure 9) in murine BAL after PBS or bleomycin treatment.
- FIG. 14 AMs in the adult human lung after transplant express ACOD1.
- A Acodl expressing AM (CD68) in BAL after male donor (RPS4Y1) to female recipient (XIST) lung transplant.
- B UMAP of Acodl expressing AMs and monocyte derived macrophages (MDM).
- C Pseudo time analysis of AM and MDM in BAL after male donor to female recipient lung transplant.
- D Pseudo-time analysis of expression of Acodl, KEAP1 and NRF2-target genes NQ.O1, TALDO1 and HMOX1 in AM and MDM after male donor to female recipient lung transplant.
- Figure 15 Pro-fibrotic genes are increased in Mo-AM compared to Tr-AM after bleomycin exposure
- B Volcano plot highlighting differentially expressed genes in WT Mo-AM vs Tr-AM at day 7 post bleomycin exposure. Genes up-regulated are shown in red and those down-regulated in blue.
- C Table highlighting fold change of fibrosis related genes of samples in (A).
- FIG. 16 BAL cell composition and collagen gene expression post adoptive transfer.
- D Representative FACS plots of CDllb+/MHC 11+ and CDllb- /MHC II- Tr-AM and Mo-AM in BAL of Acodl-/- mice after adoptive transfer of WT or Acodl-/- Mo- AMs; day 21 post bleomycin.
- WT-AT adoptive transfer of WT Mo-AMs into Acodl-/- mice
- KO-AT adoptive transfer of Acodl-/- Mo-AM into Acodl-/- mice.
- Figure 17 Exogenous itaconate limits human lung fibroblast wound healing.
- C Representative images of fibroblast wound healing during stimulation with lOmM itaconate or vehicle control, acquired using the JULI stage system. Statistical significance tested by Mann-Whitney U test of area under the curve, ** P ⁇ 0.01.
- FIG. 18 Exogenous itaconate is anti-fibrotic.
- nucleic acid sequences are written left to right in 5' to 3' orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.
- the term "capable of' when used with a verb, encompasses or means the action of the corresponding verb.
- “capable of interacting” also means interacting
- “capable of cleaving” also means cleaves
- “capable of binding” also means binds
- “capable of specifically targeting" also means specifically targets.
- the articles “a” and “an” may refer to one or to more than one (e.g. to at least one) of the grammatical object of the article. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. In this application, the use of “or” means “and/or” unless stated otherwise. Furthermore, the use of the term “including”, as well as other forms, such as “includes” and “included”, is not limiting.
- “About” may generally mean an acceptable degree of error for the quantity measured given the nature or precision of the measurements. Exemplary degrees of error are within 20 percent (%), typically, within 10%, and more typically, within 5% of a given value or range of values. Preferably, the term “about” shall be understood herein as plus or minus ( ⁇ ) 5%, preferably ⁇ 4%, ⁇ 3%, ⁇ 2%, ⁇ 1%, ⁇ 0.5%, ⁇ 0.1%, of the numerical value of the number with which it is being used.
- compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the invention.
- the term “consisting essentially of” refers to those elements required for a given invention. The term permits the presence of elements that do not materially affect the basic and novel or functional characteristic(s) of that invention (i.e. inactive or non-immunogenic ingredients).
- Embodiments described herein as “comprising” one or more features may also be considered as disclosure of the corresponding embodiments “consisting of” and/or “consisting essentially of” such features.
- Concentrations, amounts, volumes, percentages and other numerical values may be presented herein in a range format. It is also to be understood that such range format is used merely for convenience and brevity and should be interpreted flexibly to include not only the numerical values explicitly recited as the limits of the range but also to include all the individual numerical values or sub-ranges encompassed within that range as if each numerical value and sub-range is explicitly recited.
- Amino acids are referred to herein using the name of the amino acid, the three-letter abbreviation or the single letter abbreviation.
- protein and “polypeptide” are used interchangeably herein to designate a series of amino acid residues, connected to each other by peptide bonds between the alpha-amino and carboxyl groups of adjacent residues.
- protein and “polypeptide” refer to a polymer of amino acids, including modified amino acids (e.g., phosphorylated, glycated, glycosylated, etc.) and amino acid analogues, regardless of its size or function.
- modified amino acids e.g., phosphorylated, glycated, glycosylated, etc.
- amino acid analogues regardless of its size or function.
- polypeptide proteins and “polypeptide” are used interchangeably herein when referring to a gene product and fragments thereof.
- exemplary polypeptides or proteins include gene products, naturally occurring proteins, homologs, orthologs, paralogs, fragments and other equivalents, variants, fragments, and analogues of the foregoing.
- amino acid sequences of proteins of the invention are contemplated as being encompassed by the present invention, providing that the variations in the amino acid sequence(s) maintain at least 60%, at least 70%, more preferably at least 80%, at least 85%, at least 90%, at least 95%, and most preferably at least 97% or at least 99% sequence identity to the proteins of the invention or an immunogenic fragment thereof as defined anywhere herein.
- homology is used herein to mean identity.
- sequence of a variant or analogue sequence of a protein of the invention may differ on the basis of substitution (typically conservative substitution) deletion or insertion.
- Proteins of the invention may include variants in which amino acid residues from one species are substituted for the corresponding residue in another species, either at the conserved or nonconserved positions. Variants of protein molecules disclosed herein may be produced and used in the present invention. Following the lead of computational chemistry in applying multivariate data analysis techniques to the structure/property-activity relationships [see for example, Wold, et al. Multivariate data analysis in chemistry. Chemometrics-Mathematics and Statistics in Chemistry (Ed.: B. Kowalski); D.
- amino acids are referred to herein using the name of the amino acid, the three-letter abbreviation or the single letter abbreviation.
- amino acid sequence is synonymous with the term “polypeptide” and/or the term “protein”.
- amino acid sequence is synonymous with the term “peptide”.
- protein and polypeptide are used interchangeably herein.
- the conventional one-letter and three- letter codes for amino acid residues may be used.
- the 3-letter code for amino acids as defined in conformity with the IUPACIUB Joint Commission on Biochemical Nomenclature (JCBN). It is also understood that a polypeptide may be coded for by more than one nucleotide sequence due to the degeneracy of the genetic code.
- Amino acid residues at non-conserved positions may be substituted with conservative or nonconservative residues. In particular, conservative amino acid replacements are contemplated.
- a “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain.
- Families of amino acid residues having similar side chains have been defined in the art, including basic side chains (e.g., lysine, arginine, or histidine), acidic side chains (e.g., aspartic acid or glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, or cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, or tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, or histidine).
- conservatively modified variants in a protein of the invention does not exclude other forms of variant, for example polymorphic variants, interspecies homologs, and alleles.
- Non-conservative amino acid substitutions include those in which (i) a residue having an electropositive side chain (e.g., Arg, His or Lys) is substituted for, or by, an electronegative residue (e.g., Glu or Asp), (ii) a hydrophilic residue (e.g., Ser or Thr) is substituted for, or by, a hydrophobic residue (e.g., Ala, Leu, He, Phe or Vai), (iii) a cysteine or proline is substituted for, or by, any other residue, or (iv) a residue having a bulky hydrophobic or aromatic side chain (e.g., Vai, His, He or Trp) is substituted for, or by, one having a smaller side chain (e.g., Ala or Ser) or no side chain (e.g., Gly).
- an electropositive side chain e.g., Arg, His or Lys
- an electronegative residue e.g., Glu or As
- “Insertions” or “deletions” are typically in the range of about 1, 2, or 3 amino acids. The variation allowed may be experimentally determined by systematically introducing insertions or deletions of amino acids in a protein using recombinant DNA techniques and assaying the resulting recombinant variants for activity. This does not require more than routine experiments for a skilled person.
- a "fragment" of a polypeptide comprises at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 97% or more of the original polypeptide.
- proteins of the invention include both intact and modified forms of the proteins disclosed herein.
- a protein of the invention or immunogenic fragment thereof can be functionally linked (e.g. by chemical coupling, genetic fusion, noncovalent association, or otherwise) to one or more other molecular entities, such as a pharmaceutical agent, a detection agent, and/or a protein or peptide that can mediate association of a binding molecule disclosed herein with another molecule (e.g.
- Non-limiting examples of detection agents include: enzymes, such as alkaline phosphatase, glucose-6-phosphate dehydrogenase ("G6PDH”), alpha-D-galactosidase, glucose oxydase, glucose amylase, carbonic anhydrase, acetylcholinesterase, lysozyme, malate dehydrogenase and peroxidase, e.g., horseradish peroxidase; dyes; fluorescent labels or fluorescers, such as fluorescein and its derivatives, fluorochrome, rhodamine compounds and derivatives, GFP (GFP for "Green Fluorescent Protein”), dansyl, umbelliferone, phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde, and fluorescamine; fluorophores such as lanthanide cryptates and chelates, e
- enzymes such as alkaline phosphatase, glucose
- the proteins of the invention or immunogenic fragments thereof also include derivatives that are modified (e.g., by the covalent attachment of any type of molecule to the protein) such that covalent attachment does not prevent the protein from binding to antibodies specific for said protein, or otherwise impair the biological activity of the protein.
- suitable derivatives include, but are not limited to fucosylated proteins, glycosylated proteins, acetylated proteins, PEGylated proteins, phosphorylated proteins, and amidated proteins.
- a typical antibody comprises at least two "light chains” (LC) and two “heavy chains” (HC).
- the light chains and heavy chains of such antibodies are polypeptides consisting of several domains.
- Each heavy chain comprises a heavy chain variable region (abbreviated herein as "VH") and a heavy chain constant region (abbreviated herein as "CH”).
- the heavy chain constant region comprises the heavy chain constant domains CHI, CH2 and CH3 (antibody classes IgA, IgD, and IgG) and optionally the heavy chain constant domain CH4 (antibody classes IgE and IgM).
- Each light chain comprises a light chain variable domain (abbreviated herein as "VL”) and a light chain constant domain (abbreviated herein as "CL”).
- variable regions VH and VL can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR).
- CDR complementarity determining regions
- FR framework regions
- Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
- the "constant domains" of the heavy chain and of the light chain are not involved directly in binding of an antibody to a target, but exhibit various effector functions.
- CDRs Complementarity Determining Regions
- the CDRs are regions of high sequence variability, located within the variable region of the antibody heavy chain and light chain, where they form the antigen-binding site.
- the CDRs are the main determinants of antigen specificity.
- the antibody heavy chain and light chain each comprise three CDRs which are arranged non-consecutively.
- the antibody heavy and light chain CDR3 regions play a particularly important role in the binding specificity/affinity of the antibodies according to the invention and therefore provide a further aspect of the invention.
- antigen binding fragment as used herein incudes any naturally-occurring or artificially-constructed configuration of an antigen-binding polypeptide comprising one, two or three light chain CDRs, and/or one, two or three heavy chain CDRs, wherein the polypeptide is capable of binding to the antigen.
- the sequence of a CDR may be identified by reference to any number system known in the art, for example, the Kabat system (Kabat, E. A., et al., Sequences of Proteins of Immunological Interest, 5th ed., Public Health Service, National Institutes of Health, Bethesda, MD (1991); the Chothia system (Chothia &, Lesk, "Canonical Structures for the Hypervariable Regions of Immunoglobulins," J. Mol. Biol. 196, 901-917 (1987)); or the IMGT system (Lefranc et al., "IMGT Unique Numbering for Immunoglobulin and Cell Receptor Variable Domains and Ig superfamily V-like domains," Dev. Comp. Immunol. 27 , 55-77 (2003)).
- the antibodies of the invention or antigen-binding fragments thereof are preferably monoclonal antibodies. More preferably, the antibodies of the invention or antigen-binding fragments thereof are isolated monoclonal antibodies.
- humanized antibody refers to antibodies in which the framework or "complementarity determining regions” (CDRs) have been modified to comprise the CDR of an immunoglobulin of different specificity as compared to that of the parent immunoglobulin.
- CDRs complementarity determining regions
- a murine CDR may be grafted into the framework region of a human antibody to prepare the "humanized antibody.” See, e.g., Riechmann, L., et al., Nature 332 (1988) 323-327; and Neuberger, M.S., et al., Nature 314 (1985) 268-270.
- "humanized antibodies” are those in which the constant region has been additionally modified or changed from that of the original antibody to generate the properties of the antibodies according to the invention, especially in regard to Clq binding and/or Fc receptor (FcR) binding.
- chimeric antibody refers to an antibody comprising a variable region, i.e., binding region, from one source or species and at least a portion of a constant region derived from a different source or species, usually prepared by recombinant DNA techniques. Chimeric antibodies comprising a murine variable region and a human constant region are preferred. Other preferred forms of “chimeric antibodies” encompassed by the present invention are those in which the constant region has been modified or changed from that of the original antibody to generate the properties of the antibodies according to the invention, especially in regard to Clq binding and/or Fc receptor (FcR) binding. Such chimeric antibodies are also referred to as "class-switched antibodies”.
- Chimeric antibodies are the product of expressed immunoglobulin genes comprising DNA segments encoding immunoglobulin variable regions and DNA segments encoding immunoglobulin constant regions.
- Methods for producing chimeric antibodies involving conventional recombinant DNA and gene transfection techniques are well known in the art. See, e.g., Morrison, S.L., et al., Proc. Natl. Acad. Sci. USA 81 (1984) 6851-6855; US Patent Nos. 5,202,238 and 5,204,244.
- Fc region refers to the portion of a native immunoglobulin that is formed by two Fc chains.
- Each "Fc chain” comprises a constant domain CH2 and a constant domain CH3.
- Each Fc chain may also comprise a hinge region.
- a native Fc region is homodimeric.
- the Fc region may be heterodimeric because it may contain modifications to enforce Fc heterodimerization.
- IgA heavy chain constant region
- IgG is separated into four subclasses known as IgGI, lgG2, lgG3, and lgG4.
- Ig molecules interact with multiple classes of cellular receptors.
- IgG molecules interact with three classes of Fey receptors (FcyR) specific for the IgG class of antibody, namely FcyRI, FcyRII, and FcyRIII.
- FcyR Fey receptors
- the antibodies of the invention or antigen-binding fragments thereof may be any isotype, i.e. IgA, IgD, IgE, IgG and IgM, and synthetic multimers of the four-chain immunoglobulin (Ig) structure.
- Fab fragment and "Fab” are used interchangeably herein and contain a single light chain (e.g. a constant domain CL and a VL) and a single heavy chain (e.g. the constant domain CHI and a VH).
- the heavy chain of a Fab fragment is not capable of forming a disulfide bond with another heavy chain.
- a “Fab 1 fragment” contains a single light chain and a single heavy chain but in addition to the CHI and the VH, a “Fab 1 fragment” contains the region of the heavy chain between the CHI and CH2 domains that is required for the formation of an inter-chain disulfide bond. Thus, two “Fab 1 fragments” can associate via the formation of a disulphide bond to form a F(ab')2 molecule.
- a "F(ab')2 fragment” contains two light chains and two heavy chains. Each chain includes a portion of the constant region necessary for the formation of an inter-chain disulfide bond between two heavy chains.
- Fv fragment contains only the variable regions of the heavy and light chain. It contains no constant regions.
- a “single-domain antibody” is an antibody fragment containing a single antibody domain unit (e.g., VH or VL).
- a "single-chain Fv” (“scFv”) is antibody fragment containing the VH and VL domain of an antibody, linked together to form a single chain.
- a polypeptide linker is commonly used to connect the VH and VL domains of the scFv.
- TandAb® is a single-chain Fv molecule formed by covalent bonding of two scFvs in a tandem orientation with a flexible peptide linker.
- BiTE® bi-specific T cell engager
- scFvs single-chain variable fragments
- a “diabody” is a small bivalent and bispecific antibody fragment comprising a heavy (VH) chain variable domain connected to a light chain variable domain (VL) on the same polypeptide chain (VH- VL) connected by a peptide linker that is too short to allow pairing between the two domains on the same chain (Kipriyanov, Int. J. Cancer 77 (1998), 763-772). This forces pairing with the complementary domains of another chain and promotes the assembly of a dimeric molecule with two functional antigen binding sites.
- the antibodies of the invention or antigen-binding fragments thereof also include derivatives that are modified (e.g., by the covalent attachment of any type of molecule to the antibody) such that covalent attachment does not prevent the antibody from binding to its epitope, or otherwise impair the biological activity of the antibody.
- suitable derivatives include, but are not limited to fucosylated antibodies, glycosylated antibodies, acetylated antibodies, PEGylated antibodies, phosphorylated antibodies, and amidated antibodies.
- multispecific antibodies bispecific, trispecific etc.
- other conjugates e.g. with cytotoxic small molecules.
- nucleic acid refers to any molecule, preferably a polymeric molecule, incorporating units of ribonucleic acid, deoxyribonucleic acid or an analogue thereof.
- the nucleic acid can be either single-stranded or double-stranded.
- a single-stranded nucleic acid can be one nucleic acid strand of a denatured doublestranded DNA Alternatively, it can be a single-stranded nucleic acid not derived from any doublestranded DNA.
- the nucleic acid can be DNA.
- nucleic acid can be RNA Suitable nucleic acid molecules are DNA, including genomic DNA or cDNA. Other suitable nucleic acid molecules are RNA, including siRNA, shRNA, and antisense oligonucleotides.
- An exemplary, but non-limiting amino acid sequence of SDHA may comprise or consist of UniProt Accession No. P31040 (version 2 of the sequence, entry last modified 12 August 2020, provided herein as SEQ ID NO: 1).
- the corresponding nucleic acid sequence is SEQ ID NO: 2.
- An exemplary, but non-limiting amino acid sequence of SDHB may comprise or consist of UniProt Accession No. P21912 (version 3 of the sequence, entry last modified 12 August 2020, provided herein as SEQ ID NO: 3).
- the corresponding nucleic acid sequence is SEQ ID NO: 4.
- An exemplary, but non-limiting amino acid sequence of SDHC may comprise or consist of UniProt Accession No. Q99643 (version 1 of the sequence, entry last modified 12 August 2020, provided herein as SEQ ID NO: 5).
- the corresponding nucleic acid sequence is SEQ ID NO: 6.
- An exemplary, but non-limiting amino acid sequence of SDHD may comprise or consist of UniProt Accession No. 014521 (version 1 of the sequence, entry last modified 12 August 2020, provided herein as SEQ ID NO: 7).
- the corresponding nucleic acid sequence is SEQ ID NO: 8.
- An exemplary, but non-limiting amino acid sequence of ACOD1 may comprise or consist of UniProt Accession No. A6NK06 (version 1 of the sequence, entry last modified 12 August 2020, provided herein as SEQ ID NO: 9).
- the corresponding nucleic acid sequence is SEQ ID NO: 10.
- the terms “decrease”, “reduced”, “reduction”, or “inhibit” are all used herein to mean a decrease by a statistically significant amount.
- the terms “reduce,” “reduction” or “decrease” or “inhibit” typically means a decrease by at least 10% as compared to a reference level (e.g. the absence of a given treatment) and can include, for example, a decrease by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about
- “reduction” or “inhibition” encompasses a complete inhibition or reduction as compared to a reference level.
- “Complete inhibition” is a 100% inhibition (i.e. abrogation as compared to a reference level. A decrease can be preferably down to a level accepted as within the range of normal for an individual without a given disorder.
- the terms “increased”, “increase”, “enhance”, or “activate” are all used herein to mean an increase by a statically significant amount.
- the terms “increased”, “increase”, “enhance”, or “activate” can mean an increase of at least 10% as compared to a reference level, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% increase or any increase between 10-100% as compared to a reference level, or at least about a 2- fold, or at least about a 3-fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10-fold increase, or any increase between 2-fold and 10-fold or greater as compared to a reference level.
- an "increase” is a statistically significant increase in such level.
- references herein to the level of a particular molecule encompass the actual amount of the molecule, such as the mass, molar amount, concentration or molarity of the molecule.
- references to the level of a particular molecule refer to the concentration of the molecule.
- the level of a molecule may be determined in any appropriate physiological compartment.
- Preferred physiological compartments include bronchoalveolar lavage (BAL), plasma, whole blood and/or serum.
- BAL bronchoalveolar lavage
- the level of a molecule may be determined from any appropriate sample from an individual, e.g. a BAL sample plasma sample, a blood sample and/or a serum sample.
- samples which may be tested are tissue or fluid samples urine and biopsy samples.
- the invention may reference the level (e.g. concentration) of a molecule (e.g. itaconate) in the BAL and/or plasma of an individual.
- the level of a molecule pre-treatment with an agent of the invention may be interchangeably referred to as the "baseline".
- the level of a molecule may be compared with any appropriate control.
- a control may be obtained from a healthy individual or an individual without (clinically relevant) fibrosis in the tissue to be treated according to the invention.
- the control may be obtained from the same individual prior to treatment, or from a different individual with (clinically relevant) fibrosis in the same tissue type as to be treated, but wherein the different individual has not been treated with the agent, vector, composition, drug delivery system or Mo-M population of the invention.
- the level of a molecule (e.g. itaconate, collagen, fibrinogen and/or hydroxyproline) after treatment with an agent of the invention may be compared with the level of the molecule in the individual pre-treatment with the agent.
- the invention may be concerned with the relative level of the molecule (e.g. itaconate, collagen, fibrinogen and/or hydroxyproline) pre- and post-treatment.
- the level of a molecule pre-treatment e.g. itaconate, collagen, fibrinogen and/or hydroxyproline
- the level of a molecule may be measured directly or indirectly, and may be determined using any appropriate technique. Suitable standard techniques are known in the art, for example Western blotting and enzyme-linked immunosorbent assays (ELISAs).
- An individual can be one who has been previously diagnosed with or identified as suffering from or having a condition in need of treatment or one or more complications related to such a condition, and optionally, have already undergone treatment for a condition as defined herein or the one or more complications related to said condition.
- an individual can also be one who has not been previously diagnosed as having a condition as defined herein or one or more complications related to said condition.
- an individual can be one who exhibits one or more risk factors for a condition, or one or more complications related to said condition or a subject who does not exhibit risk factors.
- An "individual in need" of treatment for a particular condition can be an individual having that condition, diagnosed as having that condition, or at risk of developing that condition.
- subject means a mammalian individual.
- An “individual” may be any mammal. Generally, the individual may be human; in other words, in one embodiment, the “individual” is a human. A “individual” may be an adult, juvenile or infant. An “individual” may be male or female.
- pharmaceutically acceptable means approved by a regulatory agency of the Federal or a state government, or listed in the U.S. Pharmacopeia, European Pharmacopeia or other generally recognized pharmacopeia
- an "analogue" of a chemical structure refers to a chemical structure that preserves substantial similarity with the parent structure, although it may not be readily derived synthetically from the parent structure.
- a related chemical structure that is readily derived synthetically from a parent chemical structure is referred to as a "derivative.”
- a “hydrate” is a compound that exists in a composition with water molecules.
- the composition can include water in stoichiometric quantities, such as a monohydrate or a dihydrate, or can include water in random amounts.
- a "hydrate” refers to a solid form, i.e., a compound in water solution, while it may be hydrated, is not a hydrate as the term is used herein.
- a “solvate” is a similar composition except that a solvent other that water replaces the water.
- a solvent other that water replaces the water.
- methanol or ethanol can form an "alcoholate", which can again be stoichiometric or non- stoichiometric.
- a “solvate” refers to a solid form, i.e., a compound in solution in a solvent, while it may be solvated, is not a solvate as the term is used herein.
- prodrug as is well known in the art is a substance that can be administered to an individual where the substance is converted in vivo by the action of biochemicals within the patient's body, such as enzymes, to the active pharmaceutical ingredient.
- examples of prodrugs include esters of carboxylic acid groups, which can be hydrolyzed by endogenous esterases as are found in the bloodstream of humans and other mammals. Conventional procedures for the selection and preparation of suitable prodrug derivatives are described, for example, in "Design of Prodrugs", ed. H. Bundgaard, Elsevier, 1985.
- a “salt” as is well known in the art includes an organic compound such as a carboxylic acid, a sulfonic acid, or an amine, in ionic form, in combination with a counterion.
- acids in their anionic form can form salts with cations such as metal cations, for example sodium, potassium, and the like; with ammonium salts such as NH4+ or the cations of various amines, including tetraalkyl ammonium salts such as tetramethylammonium, or other cations such as trimethylsulfonium, and the like.
- a “pharmaceutically acceptable” or “pharmacologically acceptable” salt is a salt formed from an ion that has been approved for human consumption and is generally non-toxic, such as a chloride salt or a sodium salt.
- a “zwitterion” is an internal salt such as can be formed in a molecule that has at least two ionisable groups, one forming an anion and the other a cation, which serve to balance each other. For example, amino acids such as glycine can exist in a zwitterionic form.
- a “zwitterion” is a salt within the meaning herein.
- the compounds of the present invention may take the form of salts.
- the term “salts" embraces addition salts of free acids or free bases which are compounds of the invention.
- Salts can be “pharmaceutically-acceptable salts.
- pharmaceutically-acceptable salt refers to salts which possess toxicity profiles within a range that affords utility in pharmaceutical applications. Pharmaceutically unacceptable salts may nonetheless possess properties such as high crystallinity, which have utility in the practice of the present invention, such as for example utility in process of synthesis, purification or formulation of compounds of the invention.
- Suitable pharmaceutically-acceptable acid addition salts may be prepared from an inorganic acid or from an organic acid.
- inorganic acids include hydrochloric, hydrobromic, hydriodic, nitric, carbonic, sulfuric, and phosphoric acids.
- organic acids may be selected from aliphatic, cycloaliphatic, aromatic, araliphatic, heterocyclic, carboxylic and sulfonic classes of organic acids, examples of which include formic, acetic, propionic, succinic, glycolic, gluconic, lactic, malic, tartaric, citric, ascorbic, glucuronic, maleic, fumaric, pyruvic, aspartic, glutamic, benzoic, anthranilic, 4-hydroxybenzoic, phenylacetic, mandelic, embonic (pamoic), methanesulfonic, ethanesulfonic, benzenesulfonic, pantothenic, trifluoromethanesulfonic, 2-hydroxyethanesulfonic, p-toluenesulfonic, sulfanilic, cyclohexylaminosulfonic, stearic, alginic, p-hydroxybutyric, sal
- Suitable pharmaceutically acceptable base addition salts of compounds of the invention include, for example, metallic salts including alkali metal, alkaline earth metal and transition metal salts such as, for example, calcium, magnesium, potassium, sodium and zinc salts.
- Pharmaceutically acceptable base addition salts also include organic salts made from basic amines such as, for example, N,N-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, ethylenediamine, meglumine (N-methylglucamine) and procaine.
- Examples of pharmaceutically unacceptable base addition salts include lithium salts and cyanate salts.
- salts may be useful, for example as intermediates in the synthesis of Formula (I) compounds, for example in their purification by recrystallization. All of these salts may be prepared by conventional means from the corresponding compound according to Formula (I) by reacting, for example, the appropriate acid or base with the compound according to Formula (I).
- pharmaceutically acceptable salts refers to nontoxic inorganic or organic acid and/or base addition salts, see, for example, Lit et al., Salt Selection for Basic Drugs (1986), Int J. Pharm., 33, 201-217, incorporated by reference herein.
- SDH Succinate dehydrogenase
- TCA tricarboxylic acid cycle
- the four subunits are encoded by four genes SDHA, SDHB, SDHC and SDHD.
- SDHA encodes the main catalytic subunit, a flavoprotein (Fp) containing oxidoreductase.
- inhibitor SDH inhibits SDH
- SDH inhibitor refers to inhibition of the catalytic activity of SDH, and can be used interchangeably with the terms “inhibit SDHA”, “inhibition of SDHA” and “SDHA inhibitor”.
- the present invention provides agents which inhibit SDH for use in the treatment or prevention of tissue fibrosis.
- agents which inhibit SDH for use in the treatment or prevention of tissue fibrosis.
- Such agents and associated vectors, compositions and drug delivery systems are described herein.
- monocyte-recruited macrophage (Mo-M) populations which use the same underlying mechanisms and can also be used in the treatment or prevention of tissue fibrosis.
- the invention relates to both direct and indirect inhibition of SDH. Unless explicitly stated, references herein to inhibition of SDH encompass both direct and indirect inhibition of SDH. In some preferred embodiments, the invention relates to direct inhibition of SDH.
- Direct inhibition of SDH means inhibition of the expression and/or activity of SDH directly, i.e. without any intermediary step.
- direct inhibition of SDH may elicited by competitive or non-competitive inhibitors of the SDH enzyme or by inhibition of a gene or genes encoding the subunits of the SDH enzyme.
- Indirect inhibition of SDH means inhibition of the expression and/or activity of SDH indirectly, i.e. through the modulation or delivery of genes/enzymes upstream of SDH and/or through the generation or delivery of intermediaries which directly inhibit SDH. Indirect inhibition may be elicited by upregulating the expression of an enzyme which generates an endogenous direct inhibitor of SDH.
- indirect inhibition of SDH may involve increasing the expression and/or activity of aconitate decarboxylase 1 (ACOD1).
- ACOD1 encodes cis-aconitate decarboxylase (CAD), which catalyses the decarboxylation of cis-aconitate to itaconate. The itaconate produced inhibits SDH.
- the degree of indirect inhibition may be as defined above.
- Expression may be quantified in terms of gene and/or protein expression, and may be compared with the expression of a control (e.g. housekeeping gene or protein).
- a control e.g. housekeeping gene or protein
- the actual amount of an SDH gene, mRNA transcript and/or protein, such as the mass, molar amount, concentration or molarity of an SDH gene, mRNA transcript and/or protein, or the number of mRNA molecules per cell in a sample obtained from an individual treated according to the invention and the control may be assessed, and compared with the corresponding value from the control.
- an SDH gene and/or protein in a sample obtained from an individual treated according to the invention may be compared with that of the control without quantifying the mass, molar amount, concentration or molarity of the one or more gene and/or protein.
- control is an equivalent sample in which no inhibition of SDH expression has been effected.
- a suitable control would be a different individual to which the compound has not been administered or the same individual prior to administration of the compound.
- Conventional methods for the assessment of gene and/or protein expression are well known in the art and include RT-qPCR, ELISA, DNA microarray, RNA Seq, serial analysis of gene expression (SAGE) and western blotting.
- SDH activity may be quantified in terms of the enzyme's consumption of substrate or production of product, and may be compared with the activity of a control (i.e. recombinant enzyme of known concentration).
- Conventional methods for the assessment of SDH activity are known in the art and include colorimetric and fluorometric assays.
- the degree of inhibition may be as defined above.
- inhibition of SDH resulting in a decrease in SDH activity and/or expression of at least about 5%, at least about 10%, preferably at least about 20%, at least about 25%, at least about 30%, at least about 50%, at least about 75%, up to complete inhibition or abrogation of SDH activity and/or expression.
- An agent which inhibits SDH according to the invention may directly or indirectly inhibit SDH as described herein.
- An agent which inhibits SDH according to the invention may selectively inhibit SDH. This is typically the case for agents which directly inhibit SDH.
- selectivity may mean that the agent binds selectively (also referred to interchangeably herein as specifically) with SDH.
- binds selectively it will be understood that said agent binds to SDH, with no significant cross-reactivity to any other molecule. Cross-reactivity may be assessed by any suitable method.
- cross-reactivity of an agent which inhibits SDH with a molecule other than SDH may be considered significant if the agent binds to the other molecule at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% or 100% as strongly as it binds to SDH.
- An agent that directly inhibits SDH and that binds selectively to SDH may bind to another molecule at less than 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25% or 20% the strength that it binds to SDH.
- the agent binds to the other molecule at less than 20%, less than 15%, less than 10% or less than 5%, less than 2% or less than 1% the strength that it binds to SDH.
- Any suitable agent which inhibits SDH may be used according to the present invention.
- suitable agents include small molecules, antibodies and antigen-binding fragments thereof, peptides and peptidomimetics, nucleic acids and aptamers, as described herein.
- An agent which directly inhibits SDH may be selected from a small molecule, a nucleic acid (for example, an siRNA, shRNA, or antisense oligonucleotide), antibody or antigen-binding fragment, or an aptamer.
- a nucleic acid for example, an siRNA, shRNA, or antisense oligonucleotide
- antibody or antigen-binding fragment for example, an aptamer.
- an agent which directly inhibits SDH is a small molecule.
- An agent which indirectly inhibits SDH may be selected from a small molecule, a nucleic acid (for example, an siRNA, shRNA, or antisense oligonucleotide), antibody or antigen-binding fragment, or an aptamer.
- a nucleic acid for example, an siRNA, shRNA, or antisense oligonucleotide
- antibody or antigen-binding fragment for example, an aptamer.
- an agent that indirectly inhibits SDH increases the expression and/or activity of ACOD1.
- the degree of increase may be as defined above.
- increasing the expression and/or activity of ACOD1 refers to an increase in ACOD1 expression and/or activity of at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90%, at least about 100% or more.
- the disclosure herein regarding determining and/or quantifying the expression and or activity of SDH can also be applied in the context of ACOD1.
- ACOD1 activity may be quantified in terms of the enzyme's consumption of substrate or production of product, and may be compared with the activity of a control (i.e. recombinant enzyme of known concentration).
- Conventional methods for the assessment of ACOD1 activity are known in the art and include colorimetric and fluorometric assays.
- an agent of the invention may result in an increase in the level of itaconate within the tissue to be treated.
- the level of itaconate encompasses, the actual amount of itaconate, such as the mass, molar amount, concentration or molarity of itaconate (for a set sample size or in individual cells of said sample).
- the level of itaconate is determined in a sample obtained from an individual treated according to the invention and the control may be assessed quantitatively, and compared with the corresponding value from the control.
- the level of itaconate in a sample obtained from an individual treated according to the invention may be compared qualitatively with that of the control i.e. without quantifying the mass, molar amount, concentration or molarity of itaconate.
- a combination of agents may be used to inhibit SDH.
- a combination of agents may comprise: a direct inhibitor of SDH and an indirect inhibitor of SDH; at least two direct inhibitors of SDH; or at least two indirect inhibitors of SDH.
- Small molecules may be used as agents which inhibit SDH as described herein. In some embodiments, small molecule agents which inhibit SDH are preferred.
- small molecules are low molecular weight compounds, typically organic compounds.
- a small molecule has a maximum molecular weight of 900 g/mol, allowing for rapid diffusion across cell membranes.
- the maximum molecular weight of a small molecule is 500 g/mol.
- a small molecule has a size in the order of lnm.
- small molecule agents of the present invention contain one or more chiral centres, the compounds may exist in, and may be isolated as pure enantiomeric or diastereomeric forms or as racemic mixtures.
- the present invention therefore includes any possible enantiomers, diastereomers, racemates or mixtures thereof of small molecule agents of the invention.
- Small molecule agents of the present invention may have rotameric forms, or may not have rotational activity.
- Rotameric forms include slow rotating forms and fast rotating forms.
- fast rotating forms of the small molecule agents of the present invention are preferred.
- a small molecule agent or a salt thereof may exhibit the phenomenon of tautomerism whereby two chemical compounds that are capable of facile interconversion by exchanging a hydrogen atom between two atoms, to either of which it forms a covalent bond. Since the tautomeric compounds exist in mobile equilibrium with each other they may be regarded as different isomeric forms of the same compound.
- the invention encompasses any tautomeric form of a small molecule agent, and is not to be limited merely to any one tautomeric form.
- small molecule agents according to the invention encompass tautomers (including keto-enol and amide-imidic acid forms).
- Small molecule agents may be used in the form of pro-drugs which convert into active small molecule agents in the body, analogues or derivates, as well as in salt, hydrate and solvate forms, as defined in the Definitions section herein.
- the present inventors are the first to discover the anti-fibrotic effects of itaconate. Accordingly, in some preferred embodiments of the invention, the small molecule agent which inhibits SDH is itaconate or a derivative or analogue thereof.
- the itaconate, or derivative or analogue thereof may also be in the form of a pharmaceutically acceptable salt.
- itaconate refers to 2-methylidenebutanedioic acid as a well as derivatives or analogues thereof.
- Various synonyms of itaconate are known to the skilled person including, itaconic acid, 2-methylenesuccinic acid, 2-propene-l,2-dicarboxylic acid, methylenebutanedioic acid, methylenesuccinic acid, and propylenedicarboxylic acid, which are all encompassed by the term "itaconate”. Itaconate has been assigned Chemical Abstracts Service registry number (CAS No.) 97-65-4.
- a derivative or analogue of itaconate, or a pharmaceutically acceptable salt thereof is one that exhibits similar functional properties to itaconate.
- a derivative or analogue of itaconate, or a pharmaceutically acceptable salt thereof inhibits SDH.
- a derivative or analogue of itaconate, or a pharmaceutically acceptable salt thereof may exhibit improved SDH inhibitory activity when compared to itaconate, or may exhibit at least 50% (e.g. at least 60%, 70%, 80% or 90%) of the SDH inhibitory activity of itaconate.
- references herein to itaconate include, derivatives, analogues, hydrates, solvates, prodrug and salt forms as described herein unless explicitly states to the contrary.
- Aptamers are generally nucleic acid molecules that bind a specific target molecule. Aptamers can be engineered completely in vitro, are readily produced by chemical synthesis, possess desirable storage properties, and elicit little or no immunogenicity in therapeutic applications. These characteristics make them particularly useful in pharmaceutical and therapeutic utilities.
- aptamer refers in general to a single or double stranded oligonucleotide or a mixture of such oligonucleotides, wherein the oligonucleotide or mixture is capable of binding specifically to a target. Oligonucleotide aptamers will be discussed here, but the skilled reader will appreciate that other aptamers having equivalent binding characteristics can also be used, such as peptide aptamers.
- aptamers may comprise oligonucleotides that are at least 5, at least 10 or at least 15 nucleotides in length.
- Aptamers may comprise sequences that are up to 40, up to 60 or up to 100 or more nucleotides in length.
- aptamers may be from 5 to 100 nucleotides, from 10 to 40 nucleotides, or from 15 to 40 nucleotides in length. Where possible, aptamers of shorter length are preferred as these will often lead to less interference by other molecules or materials.
- Aptamers may be generated using routine methods such as the Systematic Evolution of Ligands by Exponential enrichment (SELEX) procedure.
- SELEX is a method for the in vitro evolution of nucleic acid molecules with highly specific binding to target molecules. It is described in, for example, US 5,654, 151, US 5,503,978, US 5,567,588 and WO 96/38579.
- the SELEX method involves the selection of nucleic acid aptamers and in particular single stranded nucleic acids capable of binding to a desired target, from a collection of oligonucleotides.
- a collection of single- stranded nucleic acids e.g., DNA, RNA, or variants thereof
- a target under conditions favourable for binding, those nucleic acids which are bound to targets in the mixture are separated from those which do not bind, the nucleic acid-target complexes are dissociated, those nucleic acids which had bound to the target are amplified to yield a collection or library which is enriched in nucleic acids having the desired binding activity, and then this series of steps is repeated as necessary to produce a library of nucleic acids (aptamers) having specific binding affinity for the relevant target.
- the invention encompasses the use of peptide and peptidomimetic agents to inhibit SDH.
- peptides, stapled peptides, peptoids and peptidomimetics that would directly or indirectly inhibit SDH is embraced by the present invention.
- Peptidomimetics are compounds which mimic a natural peptide or protein with the ability to interact with the biological target and produce the same biological effect. Peptidomimetics may have advantages over peptides in terms of stability and bioavailability associated with a natural peptide. Peptidomimetics can have main- or side-chain modifications of the parent peptide designed for biological function. Examples of classes of peptidomimetics include, but are not limited to, peptoids and p-peptides, as well as peptides incorporating D-amino acids.
- An agent which inhibits SDH may be an antibody, or an antigen binding fragment thereof as defined herein.
- An antibody according to the invention may be polyclonal or monoclonal, preferably monoclonal.
- An antibody of the invention and antigen-binding fragments thereof may be derived from any species by recombinant means.
- the antibodies or antigen-binding fragments may be mouse, rat, goat, horse, swine, bovine, chicken, rabbit, camelid, donkey, human, or chimeric versions thereof.
- non-human derived antibodies or antigen-binding fragments may be genetically or structurally altered to be less antigenic upon administration to the human patient.
- human or humanized antibodies especially as recombinant human or humanized antibodies as defined herein.
- An antibody of the invention and antigen-binding fragments thereof disclosed herein can be further modified using conventional techniques known in the art, for example, by using amino acid deletion(s), insertion(s), substitution(s), addition(s), and/or recombination(s) and/or any other modification(s) known in the art, either alone or in combination. Methods for introducing such modifications in the DNA sequence underlying the amino acid sequence of an immunoglobulin chain arc well known to the person skilled in the art.
- the antibodies of the invention or antigen-binding fragments thereof may have any antibody format.
- the antibody has the "conventional" format described above.
- the antibody can be in some embodiments a Fab fragment.
- the antibody according to the invention can also be a Fab', an Fv, an scFv, an Fd, a V NAR domain, an IgNAR, an intrabody, an IgG CH2, a minibody, a single-domain antibody, an Fcab, an scFv-Fc, F(ab')2, a di-scFv, a bi-specific T-cell engager (BiTE®), a F(ab')3, a tetrabody, a triabody, a diabody, a DVD-lg, an (scFv)2, or a mAb2.
- agents which inhibit SDH according to the invention may be nucleic acids as defined herein.
- a nucleic acid agent of the invention may inhibit SDH expression.
- nucleic acids include "antisense nucleic acids", by which is meant an RNA or DNA molecule that binds to another RNA or DNA (target RNA, DNA), whether an SDH RNA or DNA as defined herein (e.g. in the case of direct SDH inhibition), or a non-SDH RNA or DNA (e.g. in the case of indirect inhibition).
- Non-limiting examples of antisense nucleic acids include, for example, antisense RNA or DNA molecules, interference RNA (RNAi), micro RNA, decoy RNA molecules, siRNA, enzymatic RNA, therapeutic editing RNA and agonist and antagonist RNA, antisense oligomeric compounds, antisense oligonucleotides, external guide sequence (EGS) oligonucleotides, alternate splicers, primers, probes, and other oligomeric compounds that hybridize to at least a portion of the target nucleic acid (such as the SDHA gene).
- these nucleic acids may be introduced in the form of single-stranded, double- stranded, partially singlestranded, or circular oligomeric compounds.
- a nucleic acid agent of the invention may increase ACOD1 expression.
- a nucleic acid of the invention may comprise a nucleic acid sequence encoding for ACOD1 as defined herein.
- the nucleic acid sequence encoding for ACOD1 is operably linked to a promoter capable to expressing said nucleic acid sequence. Examples of inducible and non-inducible promoters are known in the art. Thus, it would be routine for one of skill in the art to select a suitable promoter.
- a nucleic acid of the invention may increase ACOD1 expression through modulation of an upstream transcriptional program.
- a nucleic acid of the invention may increase ACOD1 expression through modulation of a ZBP1- and/or RIPK-dependent transcriptional pathways. The modulation may be to up-regulate a ZBP1- and/or RIPK-dependent transcriptional pathway.
- the present invention provides a vector that expresses an agent of the invention.
- an agent of the invention may be provided by means of a vector.
- the vector may be a viral vector.
- a viral vector may be an adenovirus (of a human serotype such as AdHu5, a simian serotype such as ChAd63, ChAdOXI or ChAdOX2, or another form), an adeno-associated viral (AAV) vector or poxvirus vector (such as a modified vaccinia Ankara (MVA)).
- AAV adeno-associated viral
- VMA modified vaccinia Ankara
- ChAdOXI and ChAdOX2 are disclosed in WO2012/172277.
- ChAdOX2 is a BAC -derived and E4 modified AdC68-based viral vector.
- Viral vectors are usually non-replicating or replication impaired vectors, which means that the viral vector cannot replicate to any significant extent in normal cells (e.g. normal human cells), as measured by conventional means - e.g. via measuring DNA synthesis and/or viral titre.
- Non-replicating or replication impaired vectors may have become so naturally (i.e. they have been isolated as such from nature) or artificially (e.g. by breeding in vitro or by genetic manipulation).
- the vector is selected from a human or simian adenovirus, AAV or a poxvirus vector.
- the viral vector is incapable of causing a significant infection in an animal individual, typically in a mammalian individual such as a human or other primate.
- the invention further provides a DNA vector that expresses an agent of the invention, such as a plasmid-based DNA vaccine.
- the DNA vector is capable of expression in a mammalian cell expression system, such as an immunised cell.
- the vector may be an RNA vector, such as a self-amplifying RNA vaccine (Geall, AJ. et al., Proc Natl Acad Sci USA 2012; 109(36) pp. 14604-9).
- the present invention also provides virus-like particles (VLP) and/or fusion proteins comprising an agent of the invention, as described herein.
- VLP virus-like particles
- References herein to vectors of the invention may apply equally to VLP and/or fusion proteins of the invention.
- An agent, vector or composition of the invention may be delivered by means of a drug delivery system.
- Drug delivery systems may be used to increase delivery of an agent, vector or composition of the invention; increase uptake of an agent, vector or composition of the invention by a target cell or tissue; and/or to increase the efficacy of an agent, vector or composition of the invention.
- any appropriate drug delivery system may be used to deliver an agent, vector or composition of the invention.
- Conventional drug delivery systems are known in the art.
- appropriate drug delivery systems include liposomes, immunoliposomes, nanoparticles and conjugates.
- liposome drug delivery systems are referred to interchangeably herein as liposome-based drug delivery systems.
- phagocytic cells such as different populations of macrophages are particularly relevant in the context of fibrosis. Therefore, drug delivery systems (e.g. liposomes or nanoparticles) specifically adapted for phagocytic cells may be used according to the invention.
- drug delivery systems which specifically or preferentially target phagocytic cells may be used according to the invention.
- phosphatidyl choline cholesterol liposomes are a preferred drug delivery system of the invention.
- any suitable ratio of phosphatidyl choline: cholesterol may be used in a liposome of the invention, however, liposomes with a 70:30 molar ratio percentage of phosphatidyl choline: cholesterol are particularly preferred.
- Such liposome drug delivery systems may further be conjugated to antibodies, or antigen binding fragments thereof, which target phagocytic cell-specific cell surface markers. Liposome drug delivery systems may also be glycosyslated, preferably, mannosylated. Drug delivery systems (e.g. liposomes or nanoparticles) may be suited for delivery to phagocytic cells based on their size distribution and/or surface charge, preferably both. Typically, the drug delivery systems will have an average size of between 1 to 5 pm, preferably 1.5 to 2 pm. Therapeutic Indications
- agents, vectors, compositions and drug delivery systems as described herein are useful in the treatment of tissue fibrosis.
- Fibrosis is a pathological mechanism which occurs in numerous organs and diseases. Fibrosis results from abnormal tissue repair and is associated with persistent and/or severe tissue damage and cellular stress. Failure to adequately contain or eliminate factors triggering fibrosis can exacerbate inflammation and chronic wound-healing responses, resulting in continued tissue damage and inadequate regeneration and, ultimately, fibrosis.
- fibrosis and inflammation can occur simultaneously, the mechanisms underlying the two processes are distinct.
- IPF idiopathic pulmonary fibrosis
- fibrotic diseases Although differing in aetiology and causative mechanisms, fibrotic diseases all have abnormal and exaggerated accumulation of extracellular matrix (ECM) components, mainly fibrillar collagens. The resulting fibrosis disturbs the normal architecture of affected organs, which ultimately leads to their dysfunction and failure. Due to the common mechanism underlying fibrosis in numerous tissues and diseases, the agents, compositions and drug delivery systems of the invention are useful in treating tissue fibrosis in a range of diseases and tissue types.
- ECM extracellular matrix
- the present invention relates to the treatment of tissue fibrosis and diseases and disorders associated with tissue fibrosis.
- tissue fibrosis include pulmonary fibrosis, liver fibrosis, kidney fibrosis, intestinal fibrosis, cardiac fibrosis, myelofibrosis and/or skin fibrosis.
- the invention relates to the treatment of pulmonary (lung) fibrosis.
- diseases and disorders associated with tissue fibrosis include chronic fibrosing interstitial lung disease, connective tissue diseases (for example, scleroderma), and hepatic cirrhosis.
- the invention relates to the treatment of chronic fibrosing interstitial lung disease, even more preferably to the treatment of IPF.
- Mo-Ms monocyte derived macrophages are recruited to sites of tissue fibrosis, and that these monocyte-recruited macrophages (Mo-Ms) are less metabolically active (quiescent) than tissue-resident macrophages (Tr-Ms), which are highly oxidative.
- the inventors have surprisingly shown that Mo-Ms highly express ACOD1, and so produce high levels of itaconate, facilitating SDH inhibition. Recruitment of Mo-Ms, e.g.
- Mo-AMs monocyte- recruited airway macrophages
- pulmonary fibrosis pulmonary fibrosis
- SDH an provides one or more treatment outcome as described herein, including changing the metabolic and/or fibrotic phenotype of Tr-Ms (such as Tr-AMs).
- Tr-AMs monocyte- recruited airway macrophages
- the inventors have unexpectedly shown that transfer of Mo-Ms into the lungs of a murine model of IPF rescues the fibrotic phenotype.
- culture of AMs from IPF patients with itaconate inhibits pro-fibrotic and pro-inflammatory pathways. Therefore, inhibition of SDH according to the invention, whether by delivery of an agent, or a vector, composition or drug delivery system comprising said agent, or by delivery of a Mo-M population has therapeutic potential for tissue fibrosis.
- the invention also provides a population of Mo-Ms for use in the treatment or prevent of tissue fibrosis.
- Mo-Ms are macrophages which originate from monocytes circulating in the blood.
- Mo-Ms can be distinguished from Tr-Ms by their marker expression profile.
- Mo-Ms express (i.e. are positive for) one or more of CD14, CD163, CD206, HLA-Dr, CD71, fatty acid binding protein-4 (FABP4) and Ficolin-1. Therefore, one or more of these markers, or a combination thereof, may be used to identify Mo-Ms and hence distinguish between Mo-Ms and Tr- Ms.
- a marker expression profile of CD14, CD163, CD206, HLA-Dr, CD71, FABP4 and Ficolin-1 may be used to identify Mo-Ms.
- Mo-Ms for use according to the present invention typically express ACOD1. This is in contrast to Tr-Ms within a tissue where fibrosis is occurring, which typically do not express ACOD1, or express ACOD1 at low levels.
- Mo-Ms have an ACOD1 expression level at least 0.25 fold, at least 0.5 fold, at least 0.75 fold, at least 1 fold, at least 1.5 fold, or at least 2 fold higher than the ACOD1 expression of T r-Ms.
- Mo-Ms have an ACOD1 expression level at least 1.5 fold higher than the ACOD1 expression of Tr-Ms.
- Mo-Ms for use according to the present invention typically have low metabolic activity, or are quiescent. This may be described interchangeably herein as having a quiescent metabolic phenotype. This is in contrast to Tr-Ms within a tissue where fibrosis is occurring, are typically highly metabolically active. High levels of metabolic activity are associated with high oxygen consumption rates (OCR), whereas low levels of metabolic activity (quiescence) is associated with low OCR. Metabolic activity may also be defined in terms of a cells extracellular acidification rate (ECAR), glucose consumption, GLUT (glucose transporter) expression, isocitrate dehydrogenase (IDH2) expression, SDH expression and/or malate dehydrogenase (MDH) expression
- ECAR extracellular acidification rate
- IDH2 isocitrate dehydrogenase
- the Mo-Ms for use according to the present invention may be autologous (i.e. derived from the subject to be treated), or allogenic (i.e. from another individual of the same species).
- the Mo-Ms may be administered directly to an individual to be treated. Typically, direct administration is by intravenous infusion. Typically, about 1 x 10 s to about 5 x 10 9 Mo-Ms are delivered per administration, for example, about 1 x 10 s , 5 x 10 s , 1 x 10 7 , 5 x 10 7 , 1 x 10 8 , 5 x 10 8 , 1 x 10 9 , or 5 x 10 9 Mo-Ms per administration.
- the population of Mo-Ms may be recruited following administration of an agent, compound or composition which stimulates targeting of Mo-Ms to a tissue to be treated.
- the Mo-Ms are recruited from the individual's own circulating Mo-Ms.
- Agents capable of recruiting circulating Mo-Ms are known to those skilled in the art.
- a cytokine is used to recruit circulating Mo-Ms.
- recombinant chemokine ligand 2 (CCL2; also known as monocyte chemoattractant protein 1) may be used to recruit circulating Mo-Ms.
- Treatment may be defined as providing a treatment outcome as defined below. These definitions may apply to therapeutic and prophylactic treatments as described herein.
- Treatment may modify the metabolic and/or fibrotic phenotype of Tr-Ms.
- treatment may be defined as increasing the metabolic phenotype and/or decreasing the fibrotic phenotype of Tr-Ms.
- An increase in the metabolic phenotype of Tr-Ms may be defined as an increase in the proportion of CDllb7MHCH + Tr-Ms and/or a decrease in the proportion of CDllb /MHCir Tr- Ms.
- treatment may: (i) increase the proportion of CDllb7MHCH + Tr-Ms by at least 10%, at least 15%, at least 20% or more; and/or (ii) decrease the proportion of CDllb /MHCH’ Tr-Ms by at least 2%, at least 3%, at least 4%, at least 5% or more.
- treatment may modify the metabolic and/or fibrotic phenotype of fibroblasts within the tissue to be treated.
- treatment may be defined as decreasing the metabolic and/or fibrotic phenotype of fibroblasts within the tissue to be treated.
- a decrease in the metabolic phenotype of fibroblasts may be defined as a decrease in the OCR, maximal respiration rate and/or spare respirator capacity of the fibroblasts.
- a decrease in the fibrotic phenotype of fibroblasts may be defined as a decrease in the fibroblast proliferation rate and/or a decrease in the wound healing capacity of the fibroblasts.
- a decrease in the fibrotic phenotype of fibroblasts may also be defined in terms of the expression of fibrotic markers.
- a decrease in the fibrotic phenotype of the fibroblasts may be defined as a decrease in matrix metalloproteinase, TGFpi and/or CD71 expression.
- Treatment may modify the metabolic and/or fibrotic phenotype of Tr-Ms and fibroblasts.
- treatment may be defined as: (i) increasing the metabolic phenotype of Tr-Ms; (ii) decreasing the fibrotic phenotype of Tr-Ms; (iii) decreasing the metabolic phenotype of fibroblasts; and or (iv) decreasing the fibrotic phenotype of fibroblasts; within the tissue to be treated.
- Any combination of (i)-(iv) is encompassed by the present invention.
- treatment encompasses all of (i)-(iv).
- Treatment according to the invention may result in: (a) an improvement in the fibrosis of the tissue; (b) a decrease in tissue collagen expression, preferably Col3al, Collal and/or Col4al; (c) a decrease in tissue fibronectin (Fnl) expression; (d) a decrease in IL-ip expression in fibroblasts obtained from the tissue; and/or (e) a decrease in hydroxyproline levels.
- tissue collagen expression preferably Col3al, Collal and/or Col4al
- Fnl tissue fibronectin
- a decrease in IL-ip expression in fibroblasts obtained from the tissue and/or
- a decrease in hydroxyproline levels a decrease in hydroxyproline levels.
- Any combination of (a)-(e) is encompassed by the present invention.
- treatment encompasses all of (a)-(e).
- tissue fibrosis to be treated according to the invention is pulmonary fibrosis
- treatment may result in: (a) an improvement in lung function; (b) a reduction in the decline of forced vital capacity; (c) preservation or improvement of exercise capacity;
- An improvement in lung function may be defined as one or more of (i) an increase in force vital capacity (FVC); (ii) an increase in total lung capacity; and/or (iii) and increase in the transfer capacity of the lung for the uptake of carbon monoxide, as measured by a gas transfer (TLco) test; or (iv) any combination thereof. Any combination of (i)-(iii) is encompassed by the present invention. Preferably treatment encompasses all of (i)-(iii).
- FVC force vital capacity
- TCO gas transfer
- Treatment according to the present invention may result in any combination of the treatment outcomes as described herein.
- the invention provides an agent (as described herein), vectors and compositions comprising said agent, drug delivery systems for delivering said agent and Mo-M populations for use in the treatment or prevention of tissue fibrosis.
- Said agent inhibits SDH, and this inhibition may be direct or indirect.
- agents which indirectly inhibit SDH do so by increasing the expression and/or activity of ACOD1 as described herein.
- treat or “treating” as used herein encompasses prophylactic treatment (e.g. to prevent onset of tissue fibrosis) as well as corrective treatment (treatment of an individual already suffering from tissue fibrosis).
- the term “treat” or “treating” as used herein means corrective treatment.
- the term “treat” or “treating” encompasses treating both tissue fibrosis, symptoms thereof and diseases/disorder associated therewith. In some embodiments the term “treat” or “treating” refers to a symptom of tissue fibrosis.
- the "treatment” may be defined as providing a treatment outcome as defined herein.
- the “treatment” may modify: (i) the metabolic and/or fibrotic phenotype of Tr-Ms; and/or (ii) the metabolic and/or fibrotic phenotype of fibroblasts within the tissue to be treated; as described herein.
- “treatment” may be defined as: (i) increasing the metabolic phenotype and/or decreasing the fibrotic phenotype of Tr-Ms; and/or (ii) decreasing the metabolic and/or fibrotic phenotype of fibroblasts within the tissue to be treated; as described herein.
- An agent, vector, composition, drug delivery system or Mo-M population of the invention may be used in the treatment of an individual having Tr-Ms with reduced ACOD1 expression.
- An individual may be screened for the ACOD1 expression of their Tr-Ms prior to treatment (e.g. using a sample or biopsy of the tissue to be treated), and may be selected for treatment based on the level of expression of the Tr-Ms.
- the tissue sample used to test for Tr-M ACOD1 expression levels may be a bronchoalveolar lavage (BAL) sample.
- BAL bronchoalveolar lavage
- the level of ACOD1 expression in Tr-Ms comprised in sample e.g. a BAL sample
- the control sample may be from an individual that does not have tissue fibrosis (e.g. if BAL samples are used, pulmonary fibrosis).
- An agent, vector, composition, drug delivery system or Mo-M population of the invention may be used in the treatment of an individual having reduced levels of itaconate within the tissue undergoing fibrosis.
- An individual may be screened for the level of itaconate in the tissue to be treated prior to treatment (e.g. using a sample or biopsy of the tissue to be treated), and may be selected for treatment based on the level of itaconate in the tissue.
- the tissue sample used to test for the level may be a BAL sample.
- the level of itaconate in a BAL sample obtained from an individual to be treated is reduced compared to the level in a control BAL sample (e.g. from an individual that does not have pulmonary fibrosis).
- a “therapeutically effective amount” is any amount of an agent, vector, composition, drug delivery system or Mo-M population of the invention which, when administered alone or in combination to a patient for treating tissue fibrosis (or preventing further tissue fibrosis) or a symptom thereof or a disease associated therewith is sufficient to provide such treatment of the tissue fibrosis, or symptom thereof, or associated disease.
- a “prophylactically effective amount” is any amount of an agent, vector, composition, drug delivery system or Mo-M population of the invention that, when administered alone or in combination to an individual inhibits or delays the onset or reoccurrence of tissue fibrosis, or a symptom thereof or disease associated therewith).
- the prophylactically effective amount prevents the onset or reoccurrence of tissue fibrosis entirely. "Inhibiting" the onset means either lessening the likelihood of tissue fibrosis onset (or symptom thereof or disease associated therewith) or preventing the onset entirely.
- the terms “subject”, “individual” and “patient” are used interchangeably herein to refer to a mammalian individual.
- the individual may be human; in other words, in one embodiment, the "individual” is a human.
- the individual may not have been previously diagnosed as having tissue fibrosis (or symptom thereof or disease associated therewith).
- the individual may have been previously diagnosed as having tissue fibrosis (or symptom thereof or disease associated therewith).
- the individual may also be one who exhibits disease risk factors, or one who is asymptomatic for tissue fibrosis (or symptom thereof or disease associated therewith).
- the individual may also be one who is suffering from or is at risk of developing tissue fibrosis (or symptom thereof or disease associated therewith).
- Administration of an agent of the invention may be by any appropriate route.
- Non-limiting examples of conventional routes include inhalation; intraperitoneal, intravenous, intra-arterial, subcutaneous, and/or intramuscular injection; infusion; rectal, vaginal, topical and oral administration.
- the most appropriate administration route may be selected on the site of the fibrosis to be treated and/or prevented.
- the agent e.g. itaconate
- vector, composition, drug delivery system or Mo-M population of the invention may be administered by inhalation.
- the agent e.g. itaconate
- the agent e.g. itaconate
- vector, composition, drug delivery system or Mo-M population of the invention is administered by inhalation, preferably oropharyngeal inhalation and/or nasal inhalation.
- itaconate is administered by oropharyngeal inhalation.
- an agent e.g. itaconate
- vector, composition, drug delivery system or Mo-M population of the invention can vary from individual to individual. Determining the optimal dosage will generally involve the balancing of the level of therapeutic benefit against any risk or deleterious side effects.
- the selected dosage level will depend on a variety of factors including, the route of administration, the severity of the individual's/patient's fibrosis, and the species, sex, age, weight, condition, general health, and prior medical history of the individual/patient.
- the present inventors have identified suitable dosages of an agent of the invention, particularly itaconate, which provide the anti-fibrotic effects claimed.
- the agent, particularly itaconate is administered at a dose of about 0.1 to 20 mg/kg.
- the agent, particularly itaconate is administered at a dose of about 0.1 to 10 mg/kg, even more preferably at dose of about 5 to 10 mg/kg.
- itaconate is administered at a dose of about 5 to 10 mg/kg by oropharyngeal administration.
- an agent e.g. itaconate
- vector, composition, drug delivery system or Mo-M population is administered between about once every three months to about four times per day.
- the agent e.g. itaconate
- vector, composition or drug delivery system may be administered once every three months, once per month, twice per month, once per week, twice per week, 3 times per week, 4 times per week, 5 times per week, 6 times per week, once a day, twice a day, 3 times per day, 4 times per day or more.
- the agent (e.g. itaconate), vector, composition or drug delivery system is administered about once per day.
- An agent, vector, composition, drug delivery system or Mo-M population of the invention may have a treatment outcome as defined herein within 8-52 weeks (preferably within 36 weeks, more preferably within 24 weeks, even more preferably within 12 weeks) from baseline.
- administration of the agent, vector, composition, drug delivery system or Mo-M population of the invention may provide a treatment outcome within 36 weeks, more preferably within 24 weeks, even more preferably within 12 weeks.
- the treatment outcome may be sustained (e.g. maintained) subsequent to and/or during treatment for several weeks or months or years.
- An agent, vector, composition, drug delivery system or Mo-M population of the invention may provide a sustained treatment outcome for at least 5, 10, 12, 16, 18, 20, 22, 24, 38, 32, 36, 40, 52, 78 or 104 weeks.
- administration of an agent, vector, composition, drug delivery system or Mo-M population of the invention may provide a sustained treatment outcome for at least 5 weeks, at least 10 weeks, at least 20 weeks, or at least 52 weeks.
- agent, vector, composition, drug delivery system or Mo-M population of the invention may be used in combination with one or more additional active ingredient or therapeutic, such as another anti-fibrotic agent and/or an anti-inflammatory.
- additional active ingredient or therapeutic such as another anti-fibrotic agent and/or an anti-inflammatory.
- the agent, vector, composition, drug delivery system or Mo-M population of the invention may be used in combination with pirfenidone and/or nintedanib.
- Suitable anti-fibrotic agents which may be used in combination with an agent, vector, composition, drug delivery system or Mo-M population of the invention include pamrevlumab (an anti-connective tissue growth factor monoclonal antibody), ziritaxestat (also known as GLPG 1690, an autotaxin inhibitor), PRM-151 (a pentraxin-2 recombinant protein and GB0139 (a galectin 3 inhibitor).
- the one or more additional active ingredient or therapeutic may be administered sequentially (before or after) the agent, vector, composition, drug delivery system or Mo-M population of the invention.
- the one or more additional active ingredient or therapeutic may be administered simultaneously with the agent, vector, composition, drug delivery system or Mo-M population of the invention.
- the invention also provides method for the treatment or prevention of fibrosis comprising administering an agent, vector, composition, drug delivery system or Mo-M population of the invention which inhibits SDH.
- the invention also provides an agent, vector, composition, drug delivery system or Mo-M population of the invention which inhibits SDH for use in the manufacture of a medicament for the treatment or prevention of fibrosis.
- compositions particularly pharmaceutical compositions, comprising an agent, vector, composition, drug delivery system or Mo-M population of the invention and a pharmaceutically acceptable excipient, diluent, adjuvant, immunoregulatory agent and/or antimicrobial compound.
- the agent may be in the form of a pro-drug, analogue, derivate, salt, hydrate or solvate as described herein.
- compositions or formulations comprising an agent, vector, composition, drug delivery system or Mo-M population of the invention may further comprise one or more additional active ingredient or therapeutic, such as another anti-fibrotic agent and/or an anti-inflammatory as described herein.
- additional active ingredient or therapeutic such as another anti-fibrotic agent and/or an anti-inflammatory as described herein.
- the agent, vector, composition, drug delivery system or Mo-M population of the invention and the one or more additional active ingredient or therapeutic may be provided as a kit of parts.
- administration of immunogenic compositions, therapeutic formulations, medicaments and prophylactic formulations is generally by conventional routes, with inhalation and particularly oropharyngeal inhalation, being preferred.
- Formulation of an agent, vector, composition, drug delivery system or Mo-M population of the invention may therefore be adapted using routine practice to suit the preferred route of administration.
- Formulations suitable for distribution as aerosols are preferred, and it would be routine for one of ordinary skill in the art to prepare such formulations.
- an agent, vector, composition, drug delivery system or Mo-M population of the invention, compositions or therapeutic/prophylactic formulations and/or medicaments thereof may be prepared as injectables, either as liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in, liquid prior to injection may alternatively be prepared. The preparation may also be emulsified, or the peptide encapsulated in liposomes or microcapsules.
- the agent, vector, composition or drug delivery system of the invention may also be formulated as a dry-powder formulation.
- the active immunogenic ingredients are often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient.
- excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof.
- the composition may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and/or adjuvants which enhance the effectiveness of the vaccine.
- the carrier is a pharmaceutically-acceptable carrier.
- pharmaceutically acceptable carriers include water, saline, and phosphate-buffered saline.
- the composition is in lyophilized form, in which case it may include a stabilizer, such as BSA.
- a preservative such as thiomersal or sodium azide, to facilitate long term storage.
- additional adjuvants which may be effective include but are not limited to: complete Freunds adjuvant (CFA), Incomplete Freunds adjuvant (IFA), Saponin, a purified extract fraction of Saponin such as Quil A, a derivative of Saponin such as Q.S-21, lipid particles based on Saponin such as ISCOM/ISCOMATRIX, E.
- CFA complete Freunds adjuvant
- IFA Incomplete Freunds adjuvant
- Saponin a purified extract fraction of Saponin such as Quil A
- Q.S-21 a derivative of Saponin
- lipid particles based on Saponin such as ISCOM/ISCOMATRIX, E.
- coli heat labile toxin (LT) mutants such as LTK63 and/ or LTK72, aluminium hydroxide, N-acetyl-murarnyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-nor- muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP), N-acetylmuramyl-L-alanyl-D- isoglutaminyl-L-alanine-2-(l'-2'-dipalmitoyl-sn-glycero-3-hydroxyphosphoryl oxy)-ethylamine (CGP 19835 A, referred to as MTP-PE), and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trehalose dimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2 % squalene/ Tween
- buffering agents include, but are not limited to, sodium succinate (pH 6.5), and phosphate buffered saline (PBS; pH 6.5 and 7.5).
- suppositories include suppositories and, in some cases, oral formulations.
- traditional binders and carriers may include, for example, polyalkylene glycols or triglycerides; such suppositories may be formed from mixtures containing the active ingredient in the range of 0.5% to 10%, preferably l%-2%.
- Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders.
- the present inventors are the first to demonstrate that treating tissue fibrosis by inhibiting SDH results in quantifiable phenotypic changes in cells, particularly Tr-Ms and fibroblasts, within the tissue. Therefore, quantifying these changes in an in vitro setting has the potential to identify other agents which inhibit the progression of fibrosis, and hence have therapeutic potential for the treatment of tissue fibrosis.
- the invention also provides a method for identifying an agent which inhibits fibrosis progression comprising the steps of: (a) culturing cells in vitro; (b) adding a test agent to the cultured cells; and (c) determining a change in the metabolic phenotype of the cells in response to the test agent.
- the change in metabolic phenotype of the cells is a reduction or increase in the metabolic phenotype of the cells, as defined herein.
- test agent Any type of test agent may be employed in a method of the invention.
- the skilled person will be familiar with the various types of test agents which may be added to cultured cells in vitro.
- the test agent may be any type of agent as described herein.
- the test agent may be a small molecule, a nucleic acid agent (for example, an siRNA, a plasmid, an antisense oligonucleotide or a nucleic acid aptamer), an antibody or antibody-fragment thereof, or a peptide aptamer.
- Vectors, compositions or drug delivery systems comprising or expressing a test agent may also be employed in a screening method of the invention.
- a vector may be an adeno-associated viral vector, an adenoviral vector or a lentiviral vector comprising a nucleic sequence encoding the test agent.
- a liposomal drug delivery system comprising a test agent may be used.
- the cells are primary cells (i.e. cells derived from animal tissues) or cell lines.
- the cells used in a method of the invention may be a cell type involved in fibrosis.
- the cells may be a stromal cell or immune cell.
- fibroblasts and macrophages are particularly useful in methods of the invention.
- the cells used may be fibroblasts or macrophages, for example, Tr-Ms or Mo-Ms.
- Tr-Ms or Mo-Ms Preferably fibroblasts and/or Tr-Ms are used.
- the cells may be derived from a tissue which can develop fibrosis.
- the cells may be derived from lung tissue, or from a BAL sample.
- the cells may be derived from an individual to be treated, i.e. from an individual with fibrosis already occurring in a tissue to be treated.
- the cells may be derived from a biopsy sample of an individual with fibrosis.
- Cells, particularly Tr-Ms and/or Mo-Ms may be isolated from peripheral blood using flow cytometry.
- the metabolic phenotype assessed using a screening method of the invention may be a metabolic phenotype as described herein in the context of treatment outcomes.
- a decrease in the metabolic phenotype may be defined as a decrease in the OCR, maximal respiration rate and/or spare respirator capacity of the cells (e.g. fibroblasts).
- an increase in the metabolic phenotype may be defined as an increase in the OCR, maximal respiration rate and/or spare respirator capacity of the cells (e.g. Tr-Ms).
- An increase or decrease in metabolic phenotype may be an increase or decrease of ECAR, glucose consumption, GLUT expression, isocitrate dehydrogenase (IDH2) expression, SDH expression and/or malate dehydrogenase (MDH) expression.
- IDH2 isocitrate dehydrogenase
- SDH SDH expression
- MDH malate dehydrogenase
- the change in metabolic phenotype may be compared with a control.
- Any appropriate control may be used, and it is within the standard competency of one of ordinary skill in the art to select an appropriate control. Examples of suitable controls are described herein.
- a control may be a population of the same cell type (preferably from the same source), wherein the control cells are cultured in the same conditions as the cells exposed to the test agent, vector, composition or drug delivery system, but wherein the control cells are not exposed to the test agent, vector, composition or drug delivery system.
- a screening method of the invention may consist of the steps described herein (carried out in sequentially in the described order), or may comprise additional steps.
- the method may further comprise a step of determining a change, particularly a reduction, in the fibrotic phenotype of the cells in response to the test agent, vector, composition or drug delivery system.
- the fibrotic phenotype assessed using a screening method of the invention may be a fibrotic phenotype as described herein in the context of treatment outcomes.
- additional steps include isolating and/or the cells after exposure to the test agent, vector, composition or drug delivery system.
- SEQUENCE HOMOLOGY Any of a variety of sequence alignment methods can be used to determine percent identity, including, without limitation, global methods, local methods and hybrid methods, such as, e.g., segment approach methods. Protocols to determine percent identity are routine procedures within the scope of one skilled in the art. Global methods align sequences from the beginning to the end of the molecule and determine the best alignment by adding up scores of individual residue pairs and by imposing gap penalties. Non-limiting methods include, e.g., CLUSTAL W, see, e.g., Julie D.
- Non-limiting methods include, e.g., Match-box, see, e.g., Eric Depiereux and Ernest Feytmans, Match- Box: A Fundamentally New Algorithm for the Simultaneous Alignment of Several Protein Sequences, 8(5) CABIOS 501 -509 (1992); Gibbs sampling, see, e.g., C. E.
- percent sequence identity is determined by conventional methods. See, for example, Altschul et al., Bull. Math. Bio. 48: 603-16, 1986 and Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:10915-19, 1992. Briefly, two amino acid sequences are aligned to optimize the alignment scores using a gap opening penalty of 10, a gap extension penalty of 1, and the "blosum 62" scoring matrix of Henikoff and Henikoff (ibid.) as shown below (amino acids are indicated by the standard one-letter codes).
- the "percent sequence identity" between two or more nucleic acid or amino acid sequences is a function of the number of identical positions shared by the sequences. Thus, % identity may be calculated as the number of identical nucleotides / amino acids divided by the total number of nucleotides / amino acids, multiplied by 100. Calculations of % sequence identity may also take into account the number of gaps, and the length of each gap that needs to be introduced to optimize alignment of two or more sequences. Sequence comparisons and the determination of percent identity between two or more sequences can be carried out using specific mathematical algorithms, such as BLAST, which will be familiar to a skilled person.
- Substantially homologous polypeptides are characterized as having one or more amino acid substitutions, deletions or additions. These changes are preferably of a minor nature, that is conservative amino acid substitutions (as described herein) and other substitutions that do not significantly affect the folding or activity of the polypeptide; small deletions, typically of one to about 30 amino acids; and small amino- or carboxyl-terminal extensions, such as an amino-terminal methionine residue, a small linker peptide of up to about 20-25 residues, or an affinity tag.
- non-standard amino acids such as 4- hydroxyproline, 6-N-methyl lysine, 2-aminoisobutyric acid, isovaline and a -methyl serine
- a limited number of non-conservative amino acids, amino acids that are not encoded by the genetic code, and unnatural amino acids may be substituted for polypeptide amino acid residues.
- the polypeptides of the present invention can also comprise non-naturally occurring amino acid residues.
- Non-naturally occurring amino acids include, without limitation, trans-3-methylproline, 2,4- methano-proline, cis-4-hydroxyproline, trans-4-hydroxy-proline, N-methylglycine, allo-threonine, methyl-threonine, hydroxy-ethylcysteine, hydroxyethylhomo-cysteine, nitro-glutamine, homoglutamine, pipecolic acid, tert-leucine, norvaline, 2-azaphenylalanine, 3-azaphenyl-alanine, 4- azaphenyl-alanine, and 4-fluorophenylalanine.
- Several methods are known in the art for incorporating non-naturally occurring amino acid residues into proteins.
- an in vitro system can be employed wherein nonsense mutations are suppressed using chemically aminoacylated suppressor tRNAs.
- Methods for synthesizing amino acids and aminoacylating tRNA are known in the art. Transcription and translation of plasmids containing nonsense mutations is carried out in a cell free system comprising an E. coli S30 extract and commercially available enzymes and other reagents. Proteins are purified by chromatography. See, for example, Robertson et al., J. Am. Chem. Soc. 113:2722, 1991; Ellman et al., Methods Enzymol.
- coli cells are cultured in the absence of a natural amino acid that is to be replaced (e.g., phenylalanine) and in the presence of the desired non-naturally occurring amino acid(s) (e.g., 2-azaphenylalanine, 3- azaphenylalanine, 4-azaphenylalanine, or 4-fluorophenylalanine).
- the non-naturally occurring amino acid is incorporated into the polypeptide in place of its natural counterpart. See, Koide et al., Biochem. 33:7470-6, 1994.
- Naturally occurring amino acid residues can be converted to non-naturally occurring species by in vitro chemical modification. Chemical modification can be combined with site-directed mutagenesis to further expand the range of substitutions (Wynn and Richards, Protein Sci. 2:395-403, 1993).
- a limited number of non-conservative amino acids, amino acids that are not encoded by the genetic code, non-naturally occurring amino acids, and unnatural amino acids may be substituted for amino acid residues of polypeptides of the present invention.
- Essential amino acids in the polypeptides of the present invention can be identified according to procedures known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham and Wells, Science 244: 1081-5, 1989).
- Sites of biological interaction can also be determined by physical analysis of structure, as determined by such techniques as nuclear magnetic resonance, crystallography, electron diffraction or photoaffinity labeling, in conjunction with mutation of putative contact site amino acids.
- LGLLPAAYLNPCSAM DYSLAAALTLHGHWGLGQVVTDYVHGDALQKAAKAGLLALSALTFAGLCYFNYHDVGICK
- SEQ ID NO: 8 Human SDHD nucleic acid sequence ATGGCGGTTCTCTGGAGGCTGAGTGCCGTTTGCGGTGCCCTAGGAGGCCGAGCTCTGTTG
- Bronchoscopy of the right middle lobe was performed after informed consent as approved by an external Research Ethics Committee for ILD subjects (Ref. Nos. 10/H0720/12 and 15/SC0101) and healthy control subjects (Ref. No. 15-LO-1399) according to the Royal Brompton Hospital protocol (Royal Brompton & Harefield NHS Foundation Trust, 2016). Bronchoscopies were performed with subjects under a light sedation with midazolam in combination with local anesthesia with lidocaine. Four 60-ml aliquots of warmed sterile saline were instilled in the right middle lung lobe and aspirated by syringe and lavage aliquots collected after each instillation were pooled for each patient. Volume and BAL appearance were recorded for all samples.
- HBEs were cultured in bronchial epithelial cell growth (BEGM) medium (Lonza) to passage four.
- MACS enriched human AM were cultured in complete RPMI (10% FBS, lOOU/ml penicillin/streptomycin, Gibco, ThermoFisher) for 24 hrs.
- Fibroblasts and AM were cultured with lOmM itaconate in complete medium for 24hrs prior to cell lysis in RLT buffer (QIAGEN) containing 1% 2-Mercaptoethanol (Sigma Aldrich).
- Acodl /_ mice and littermate controls were bred on a C57BL/6 background. Unless otherwise stated, all mice were between 8 and 12 weeks of age. Mice were housed in specific-pathogen-free conditions and given food and water ad libitum. All procedures were approved by the United Kingdom Home Office and conducted in strict accordance with the Animals (Scientific Procedures) Act 1986. The Imperial College London Animal Welfare and Ethical Review Body (AWERB) approved this protocol. All surgery was performed under ketamine and sodium pentobarbital anaesthesia and all efforts were made to minimize suffering.
- mice were administered either 0.05U (lU/ml solution dissolved in PBS) of bleomycin sulphate (Sigma Aldrich) or 50pl PBS via the oropharyngeal route at day 0 and culled after 7, 21 or 42 days.
- mice were administered 0.25mg/kg (ImM solution dissolved in PBS, 50pl) itaconic acid (Sigma Aldrich) or PBS via the oropharyngeal route twice a week, beginning 10 days after of bleomycin administration.
- Viable cryopreserved BAL cells were sorted on a BD Influx sorter (Becton Dickinson) as previously described (Byrne et al., 2020) and retained on ice. Briefly, cells at a concentration of 800 - 1,000 cells/pl were loaded onto lOx Genomics single cell 3' chips along with the RT mastermix (Chromium Single Cell 3' Library, v2, PN-120233, 10X Genomics) according to manufacturer's instructions to generate single-cell gel beads in emulsion. RT was performed using a C1000 Touch Thermal Cycler with a Deep Well Reaction Module (Bio-Rad; 55°C for 2 h; 85°C for 5 min; hold 4°C).
- DynaBeads MyOne Silane Beads, Thermo Fisher Scientific
- SPRIselect beads Beckman Coulter
- Amplified cDNA was sheared to ⁇ 200 base pairs with a Covaris S2 instrument using the manufacturer's recommended parameters.
- Sequencing libraries were generated with unique sample indices and sequenced on a Illumina NewtSeq 500 (NextSeq control software v2.0.2/ Real Time Analysis v2.4.11) using a 150-cycle NextSeq 500/550 High Output Reagent Kit v2 (FC-404-2002; Illumina) in stand-alone mode as follows: 98 bp (read 1), 14 bp (17 index), 8 bp (15 index), and 485 10 bp (read 2).
- the Cell Ranger Single Cell Software Suite (10X Genomics, v2.0.0) was used to process the sequencing data into transcript count tables.
- Raw base call files were demultiplexed using the Cell Ranger mkfastq programme into sample-specific FASTQ files, which were then processed using the Cell Ranger count pipeline. Subsequent analysis was performed as described previously (Byrne et al., 2020).
- Freeze dried BAL samples were spiked with ds-labelled methylmalonic acid (d3-MMA, synthesized in house) and derivatized with 30pl methoxyamine hydrochloride (Sigma-Aldrich, 20mg/ml in pyridine, 40°C for 20min) to modify any carbonyls (multi-component method). After cooling, 70pl of N,O-bis(trimethylsilyl)trifluoroacetamide containing 1% trimethylchlorosilane (BSTFA Sigma-Aldrich) were added and the mixture incubated for 30 minutes at 60°C to effect trimethylsilylation of the hydroxy functions. Finally, the supernatants from centrifuged reaction mixtures were transferred to injection vials.
- ds-labelled methylmalonic acid d3-MMA, synthesized in house
- 30pl methoxyamine hydrochloride Sigma-Aldrich, 20mg/ml in pyridine, 40°C for 20min
- GC/MS analysis was performed on an Agilent 6890 gas chromatograph coupled to a 5973 MSD quadrupole mass spectrometer. Samples were injected in splitless mode with the inlet maintained at 280°C. Separation of the derivatives was performed on a DB-1701 capillary column 30m x 250pm x 0.25pm (Agilent Technologies) using a three-stage temperature program to optimize the separation. Mass spectral data was acquired by selected ion monitoring (SIM) of m/z 259 (quantifier) and m/z 215 (qualifier) at approx. 6 min retention time. A five-level calibration plot was constructed over the concentration range 0-16 ng/ml. Quantitation was achieved by interpolation using the regression equation of the calibration curve. All data processing and concentration calculations were performed using Agilent MassHunter (v. B.07.01) software.
- Lung function measurements were performed using the Flexivent system (Scireq, Montreal, Canada). After induction of anaesthesia with an i.p. injection of Pentobarbitone (50 mg/Kg, Sigma, UK) and i.m. injection of Ketamine (200 mg/Kg) (Fortdodge Animal Health Ltd, Southampton, UK), mice were tracheotomised and attached to the Flexivent ventilator via a blunt-ended 19-gauge needle. Mice were ventilated using the following settings; tidal volume of 7 ml/Kg body weight, 150 breaths/minute; positive end-expiratory pressure approximately 2cm H2O. Standardisation of lung volume history was done by performing two deep inflations.
- BAL fluid was centrifuged (700 X g, 5 min, 4°C); cells were resuspended in 0.5 ml complete media (RPMI + 10% fetal calf serum [FCS], 2 mM L-glutamine, 100 U/ml penicillin/ streptomycin). Cells were counted and pelleted onto glass slides by cytocentrifugation (5 xio 4 cells/slide).
- one finely chopped left lobe of lung was incubated at 37°C for 1 h in digest reagent (0.15 mg/ml collagenase type D, 25 pg/ml DNase type I) in complete RPMI media.
- digest reagent (0.15 mg/ml collagenase type D, 25 pg/ml DNase type I) in complete RPMI media.
- the recovered cells were filtered through a 70-pm nylon sieve, washed twice, resuspended in 1ml complete media, and counted in a haemocytometer prior to cytocentrifugation; lung cell counts are quoted as total cell number/ml of this suspension.
- mice Female WT or Acodl-/- mice were dosed with 0.05U bleomycin via the oropharyngeal route and lavaged at day 7 post bleomycin to obtain monocyte-recruited AMs (Mo-AMs). Cells recovered from bronchoaleolar lavage were stained with extracellular antibodies as described above and live, CD45 + , CD64 + , CDllc + , SigF int Mo-AMs were isolated by FACS sorting as shown in the gating strategy in Figure 9. Subsequently, 50,000 WT or Acodl /_ Mo-AMs were administered via the oropharyngeal route to male Acodl /_ mice, which had been dosed with bleomycin 7 days prior . Mice were sacrificed at day 21 post initial bleomycin exposure.
- Hydroxyproline was measured using lOmg of tissue from the inferior lobe of murine samples using a Hydroxyproline Assay Kit (Sigma Aldrich), as per manufacturer's instructions and fold change of bleomycin/PBS groups was calculated. Histology
- RNA from the post-caval lobe was extracted using the QIAGEN RNeasy Mini Kit plus (QIAGEN) or using the QIAGEN RNeasy Micro Kit plus for total RNA from cell cultures and BAL cells.
- Total RNA was reverse transcribed into cDNA using the High Capacity cDNA Reverse Transcription kit (Life Technologies), or GoScript reverse transcription system (Promega) for AMs, according to manufacturer's instructions.
- Real-time PCR was performed using fast-qPCR mastermix (Life technologies) on a Viia-7 instrument (Applied Biosciences) with Taqman primers for murine acodl, col-lal, colSal, col4al, fnl, mmp2 or human acodl, cdl63, fnl, IL-16, mmpl, mmp9 using actb (Life Technologies) as housekeeping gene.
- actb Life Technologies
- total RNA (0.08 pg) of FACS sorted Mo-AMs or Tr-AMs was reverse transcribed into cDNA using the RT 2 first- strand synthesis kit as per manufacturer's instructions (QIAGEN).
- Gene expression of 84 genes in murine fibrosis was assessed using fast-qPCR SYBR Green Master Mix (Qiagen, Germany) and mouse fibrosis 96-well genearray (120Z, QIAGEN) on a ViiA-7 instrument. Gene expression was analysed using the QIAGEN data analysis centre.
- Oxygen Consumption Rate (OCR) and extracellular acidification rate (ECAR) were measured in XF medium (nonbuffered RPMI containing 2mM glutamine, ImM pyruvate and lOmM glucose, pH 7.4, Agilent) using the XFp extracellular flux analyser (Agilent).
- OCR and ECAR were measured under basal conditions and after the sequential addition of 1.5 pM Oligomycin, 2.0 pM FCCP and 0.5 pM Rotenone/Antimycin A (mito stress test, Agilent), which enabled the calculation of spare respiratory capacity from basal and maximal respiration as a result of OxPhos.
- ACOD1 mRNA in the human lung expression levels were assessed in primary airway macrophages (AMs), lung fibroblasts (HLF) and human bronchial epithelial cells (HBEs) from healthy volunteers and IPF patients.
- AMs were enriched using magnetic associated cell sorting (MACS) based on CD206 expression, as this marker has been identified as most expressed on human airway macrophages (see Tables 1 and 2 for patient demographics).
- MCS magnetic associated cell sorting
- Table 1 Subject demographics of samples used for qPCR analysis ( Figure 1A).
- Table 1 shows the sex, age, drug-treatment, FEV1, FEV1 % predicted, forced vital capacity
- Table 2 Subject demographics of samples used for GC-MS analysis ( Figure IB).
- Table 2 shows the sex, age, drug-treatment, FEV1, FEV1 % predicted, forced vital capacity
- Example 2 Acodl deficiency results in worsened pulmonary fibrosis in mice
- Acodl reached maximum-expression levels at d21 post bleomycin, corresponding with both inflammation and peak fibrosis (Figure ID). Furthermore, itaconate levels in BAL were assessed by targeted gas chromatography-mass spectrometry (GC-MS) at these different time points. Compared to PBS controls, itaconate was significantly increased at d7 and d21 post bleomycin and returned to baseline levels at d42 ( Figure IE). In order to determine whether Acodl played a role in the establishment or severity of fibrosis, the response of Acod1-deficient mice to bleomycin was assessed.
- GC-MS gas chromatography-mass spectrometry
- Adaptive immunity did not appear to be altered in Acodl' 7 ' mice compared to WT controls, with no alteration in T- or NK-cells at any time-point ( Figure 10G and H).
- Acodl' 7 ' mice showed increased expression of Collagen-(Col)3al and Fibronectin-1 (Fn- 1) (Figure 2A), compared to WT controls at day 21, but not at d7/42 ( Figure 11A and B). No statistically significant change in lung expression of Collal or Col4al was observed at any time point assessed in this model (Figure 2A and Figure 11A - B).
- Ashcroft scoring of Sirius red stained lung slices indicated that pathology did not change in Acodl' 7 ' mice at day 21 post bleomycin compared to WT (Figure 11C).
- Acodl' 7 ' mice had enhanced pulmonary fibrosis compared to WT controls, characterized by increased lung hydroxyproline levels (Figure 2B) and Ashcroft scores (Figure 2C and D). Consistent with these findings, Acodl' 7 ' mice showed increased levels of superoxide in in the CD45 + compartment of whole lung tissue in comparison to WT ( Figure 2E, Figure 9B), further suggesting more severe disease in Acodl' 7 '.
- Mo-AMs monocyte-derived AMs
- Tr-AMs fetally derived tissue resident AMs
- WT Mo-AMs had similar levels of oxidative phosphorylation (OxPhos) and glycolysis (ECAR) compared to Acodl ' cells ( Figure 3D - G). However, Acodl Tr-AMs had reduced OCR (Figure 3H), maximal respiration (Figure 31) and spare respiratory capacity (SRC, Figure 3J) in comparison to WT Tr-AMs, while basal ECAR remained unchanged ( Figure 3K). Together these results indicate that during lung fibrosis in mice, recruited Mo-AMs are characterized by a quiescent metabolic phenotype and in contrast, resident Tr-AMs are highly oxidative.
- OxPhos oxidative phosphorylation
- ECAR glycolysis
- CAD expression is a critical regulator of metabolism in tissue resident AMs during lung fibrosis, as itaconate deficiency leads to decreased oxidative phosphorylation.
- Analysis of ACOD-expressing cells in a male donor to female recipient showed a subset of ACOD1 expressing AMs, which are monocyte derived (MDMs; Figure 14A - B, as they do not express the male cell identifier RPS4Y1 but do express the female identifier gene XIST).
- Example 4 Acodl deficient tissue resident AMs are more pro-fibrotic post bleomycin
- Tr-AMs and Mo-AMs differed in their response to bleomycin-induced lung fibrosis, with Mo-AMs comparatively high expressers of genes implicated in fibrotic signalling processes such as Colla2, Transforming growth factor 62 (Tgf62) and Ccr2 ( Figure 15A and B). Comparing Acodl 7 ' and WT sorted airway macrophages, the data indicate that itaconate deficiency significantly increased gene expression of fibrosis related genes in Tr-AMs ( Figure 4A), while it downregulated the expression of only two genes in Mo-AMs ( Figure 4B).
- the annotated genes are those that showed significant change in expression or at least 10-fold increase in Acodl' 7 ' AMs, compared to WT cells.
- IL-1 Integrin linked kinase
- Ilk Integrin linked kinase
- Tr-AMs pro-fibrotic mediators including CCAAT enhancer binding protein 6 (Cebpb), TgfBrl and Smad7 were significantly increased in Acodl' 7 ' Tr-AMs compared to WT cells ( Figure 4D).
- Example 5 Adoptive transfer of WT, but not Acodl 7 ' Mo-AMs, into the airways of Acodl 7 ' bleomycin treated mice rescued the fibrotic phenotype
- Example 6 Exogenous itaconate limits human lung fibroblast wound healing
- Fibroblasts are the principle effector cell during lung fibrosis and the main source of the excessive extracellular matrix deposition seen during the disease (Kendall and Feghali-Bostwick, 2014, Front. Pharmacology, 5:1-13), however our data indicate that these cells do not express Acodl (data not shown). Since macrophages are known to regulate the pro-fibrotic activity of fibroblasts in the lung (Byrne et al., 2016, Trends Mol. Med. 22:303-316) and itaconate is secreted into the airways ( Figures IB and IE), it was next assessed whether itaconate could directly influence fibrosis by limiting the metabolic and pro-fibrotic activity of human lung fibroblasts (HLF).
- HLFs After exposure to itaconate, HLFs showed significantly reduced proliferative capacity over 72h in both cells derived from healthy donors (Figure 6D) as well IPF patients ( Figure 17A), while the ability to close a standardized wound over a 48h period was decreased in healthy HLFs (Figure 6E) but not in IPF fibroblasts ( Figure 17B and C). Furthermore, culture with itaconate downregulated the gene expression of IL-l and FN-1 in healthy HLFs ( Figure 5F). Taken together these data suggest that itaconate impacts fibroblast metabolic phenotype, proliferation and wound healing thereby limiting the severity of pulmonary fibrosis.
- Example 7 Inhaled itaconate is anti-fibrotic
- Acod1/itaconate pathway in the pathogenesis of pulmonary fibrosis.
- AM phenotype is a critical component of lung immunity and manipulation of AM phenotype can have drastic consequences for lung health. Itaconate has emerged as a key autocrine immunoregulatory component involved in activation of bone-marrow derived macrophages (BMDMs), however to-date little was known regarding the specific role of itaconate in highly specialized tissue resident macrophage populations during chronic disease, such as those found in the airways in IPF. Itaconate is a critical component of pulmonary responses to MTb infection as both global Acodl / and myeloid-specific Acodl / knockouts rapidly succumb to infection.
- BMDMs bone-marrow derived macrophages
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